[==========] Running 57 tests from 4 test cases. [----------] Global test environment set-up. [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision) Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 5 steps. Potential Energy = -4.79910464433593e+01 Maximum force = 1.86297359800816e+02 on atom 13 Norm of force = 8.77219867200309e+01 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (223 ms) [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision) Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 F-max = 3.02331e+02 on atom 3 F-Norm = 1.18024e+02 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. Potential Energy = -5.58622539552362e+01 Maximum force = 4.27274823589661e+02 on atom 13 Norm of force = 1.84530029788224e+02 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (202 ms) [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 20503 of the 20503 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 22.00 NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision) Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 5 steps. Potential Energy = 3.19376899489615e+02 Maximum force = 9.99884921027275e+03 on atom 9 Norm of force = 4.61669565061010e+03 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (127 ms) [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 20503 of the 20503 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' turning H bonds into constraints... NOTE 3 [file glycine_vacuo.top, line 12]: For accurate cg with LINCS constraints, lincs-order should be 8 or more. Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 22.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision) Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 F-max = 2.41575e+04 on atom 10 F-Norm = 1.18451e+04 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. Potential Energy = 1.51743017875794e+02 Maximum force = 7.42089573427939e+03 on atom 9 Norm of force = 3.56929298621805e+03 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (116 ms) [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' turning all bonds into constraints... NOTE 3 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. Cleaning up constraints and constant bonded interactions with virtual sites Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Converted 15 Constraints with virtual sites to connections, 7 left Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 23.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision) Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 5 steps. Potential Energy = -1.56984194095140e+02 Maximum force = 4.56923625858680e+02 on atom 17 Norm of force = 1.83258377483257e+02 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (64 ms) [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' turning all bonds into constraints... NOTE 3 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. NOTE 4 [file unknown]: For accurate cg with LINCS constraints, lincs-order should be 8 or more. Cleaning up constraints and constant bonded interactions with virtual sites Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Converted 15 Constraints with virtual sites to connections, 7 left Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 23.00 NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision) Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 F-max = 1.06800e+03 on atom 28 F-Norm = 4.26922e+02 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. Potential Energy = -1.69410778941235e+02 Maximum force = 2.18225948179602e+02 on atom 17 Norm of force = 7.92068036008141e+01 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (68 ms) [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (800 ms total) [----------] 6 tests from MinimizersWork/EnergyMinimizationTest [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 33.00 This run will generate roughly 0 Mb of data There were 2 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision) Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 writing lowest energy coordinates. Steepest Descents converged to Fmax < 10 in 1 steps Potential Energy = -9.74257075835447e-01 Maximum force = 4.01322929015132e+00 on atom 1 Norm of force = 1.63839399694378e+00 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (60 ms) [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 33.00 This run will generate roughly 0 Mb of data There were 2 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision) Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 F-max = 4.01323e+00 on atom 1 F-Norm = 1.63839e+00 writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps Potential Energy = -9.90642313893957e-01 Maximum force = 2.57812909491105e+00 on atom 1 Norm of force = 1.05251679559258e+00 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (56 ms) [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. WARNING 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 33.00 This run will generate roughly 0 Mb of data There were 2 notes There was 1 warning Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision) Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. Low-Memory BFGS Minimizer: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Using 10 BFGS correction steps. F-max = 4.01323e+00 on atom 1 F-Norm = 1.63839e+00 writing lowest energy coordinates. Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps Potential Energy = -9.90642313893957e-01 Maximum force = 2.57812909491105e+00 on atom 1 Norm of force = 1.05251679559258e+00 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (60 ms) [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 20503 of the 20503 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision) Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 5 steps. Potential Energy = 3.19395484629892e+02 Maximum force = 9.97041707215794e+03 on atom 9 Norm of force = 4.62274878672163e+03 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (132 ms) [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Generated 20503 of the 20503 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision) Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 F-max = 2.41672e+04 on atom 10 F-Norm = 1.19357e+04 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. Potential Energy = 1.56258793634225e+02 Maximum force = 7.50181017498405e+03 on atom 9 Norm of force = 3.61390332570589e+03 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (128 ms) [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. WARNING 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. Generated 20503 of the 20503 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Glycine' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 3 notes There was 1 warning Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision) Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. Low-Memory BFGS Minimizer: Tolerance (Fmax) = 1.00000e+01 Number of steps = 4 Using 10 BFGS correction steps. F-max = 2.41672e+04 on atom 10 F-Norm = 1.19357e+04 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps. Potential Energy = 1.84722734378548e+03 Maximum force = 2.12615356182376e+04 on atom 9 Norm of force = 1.01988549359681e+04 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 /dev/shm/gromacs-2019.1/src/testutils/refdata.cpp:922: Failure In item: /glycine_no_constraints_vacuo/l-bfgs/Potential/Time 4.000000 Step 4 in frame 2 Actual: 1847.2273437854799 Reference: 1847.227343785434 Difference: 4.59295e-11 (202 double-prec. ULPs, rel. 2.49e-14) Tolerance: abs. 4.44089e-11, 100 ULPs Google Test trace: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/energycomparison.cpp:126: Comparing Potential in Time 4.000000 Step 4 in frame 2 /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/minimize.cpp:121: Comparing 'l-bfgs' energy minimization for simulation 'glycine_no_constraints_vacuo' Last energy frame read 2 time 4.000 [ FAILED ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5, where GetParam() = ("glycine_no_constraints_vacuo", "l-bfgs") (124 ms) [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (560 ms total) [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp, line 28]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 4 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.004 0.004 98.6 (ns/day) (hour/ns) Performance: 362.217 0.066 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun 'Argon', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_normal.trr' trr version: GMX_trn_file (double precision) Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.001 94.0 (ns/day) (hour/ns) Performance: 2524.833 0.010 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (111 ms) [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp, line 28]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 33.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: NVE simulation: will use the initial temperature of 68.810 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 4 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.002 0.002 97.9 (ns/day) (hour/ns) Performance: 694.778 0.035 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun 'Argon', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 Core t (s) Wall t (s) (%) Time: 0.001 0.001 94.8 (ns/day) (hour/ns) Performance: 1955.744 0.012 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (113 ms) [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp, line 28]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.002 0.002 97.8 (ns/day) (hour/ns) Performance: 629.853 0.038 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun 'Argon', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 11 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.001 93.7 (ns/day) (hour/ns) Performance: 2330.028 0.010 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (115 ms) [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp, line 28]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 1 of the 1 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Argon' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 33.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data There were 3 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun 'Argon' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.003 0.003 98.3 (ns/day) (hour/ns) Performance: 497.585 0.048 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun 'Argon', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.001 93.9 (ns/day) (hour/ns) Performance: 2267.425 0.011 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (115 ms) [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp, line 28]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.004 0.004 98.4 (ns/day) (hour/ns) Performance: 399.338 0.060 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun 'spc2', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 14 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.001 94.6 (ns/day) (hour/ns) Performance: 2064.542 0.012 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (281 ms) [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp, line 28]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 27.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: NVE simulation: will use the initial temperature of 398.997 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.004 0.004 98.8 (ns/day) (hour/ns) Performance: 348.233 0.069 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun 'spc2', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 15 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.001 94.1 (ns/day) (hour/ns) Performance: 2336.213 0.010 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (270 ms) [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp, line 28]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 100, rlist from 0.733 to 0.824 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.004 0.004 98.3 (ns/day) (hour/ns) Performance: 399.080 0.060 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 100, rlist from 0.733 to 0.824 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun 'spc2', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 15 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.001 93.9 (ns/day) (hour/ns) Performance: 2288.482 0.010 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (276 ms) [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp, line 28]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 27.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun 'spc2' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.003 0.003 97.8 (ns/day) (hour/ns) Performance: 573.772 0.042 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun 'spc2', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 22 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.001 94.8 (ns/day) (hour/ns) Performance: 1997.598 0.012 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (270 ms) [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp, line 28]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' turning all bonds into constraints... NOTE 4 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. Cleaning up constraints and constant bonded interactions with virtual sites Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Converted 15 Constraints with virtual sites to connections, 7 left Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 23.00 NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: NVE simulation: will use the initial temperature of 456.887 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K NOTE 6 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: There are 9 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 7 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 7 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun 'Alanine dipeptide in vacuo' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.003 0.004 97.3 (ns/day) (hour/ns) Performance: 414.771 0.058 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.001 96.3 (ns/day) (hour/ns) Performance: 1380.371 0.017 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (127 ms) [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp, line 28]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' turning all bonds into constraints... NOTE 4 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. Cleaning up constraints and constant bonded interactions with virtual sites Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Converted 15 Constraints with virtual sites to connections, 7 left Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 23.00 NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: NVE simulation: will use the initial temperature of 456.887 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K NOTE 6 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: There are 9 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 7 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 7 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun 'Alanine dipeptide in vacuo' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.005 0.005 98.4 (ns/day) (hour/ns) Performance: 316.512 0.076 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 16 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.001 96.5 (ns/day) (hour/ns) Performance: 1468.206 0.016 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (133 ms) [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp, line 28]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' turning all bonds into constraints... NOTE 4 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. Cleaning up constraints and constant bonded interactions with virtual sites Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Converted 15 Constraints with virtual sites to connections, 7 left Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 23.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: There are 9 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 6 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 6 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun 'Alanine dipeptide in vacuo' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.004 0.004 98.2 (ns/day) (hour/ns) Performance: 403.286 0.060 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 14 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.001 96.5 (ns/day) (hour/ns) Performance: 1440.738 0.017 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (139 ms) [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp, line 28]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' turning all bonds into constraints... NOTE 4 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. Cleaning up constraints and constant bonded interactions with virtual sites Removed 18 Angles with virtual sites, 21 left Removed 10 Proper Dih.s with virtual sites, 44 left Converted 15 Constraints with virtual sites to connections, 7 left Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 23.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: There are 9 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 6 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 6 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun 'Alanine dipeptide in vacuo' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.005 0.005 98.6 (ns/day) (hour/ns) Performance: 318.262 0.075 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 14 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.001 96.7 (ns/day) (hour/ns) Performance: 1459.510 0.016 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (137 ms) [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (2088 ms total) [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.004 0.004 98.6 (ns/day) (hour/ns) Performance: 351.251 0.068 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 12 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.001 96.7 (ns/day) (hour/ns) Performance: 1062.354 0.023 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (120 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.005 0.005 98.6 (ns/day) (hour/ns) Performance: 319.865 0.075 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.001 96.7 (ns/day) (hour/ns) Performance: 1253.427 0.019 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (120 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.005 0.005 98.6 (ns/day) (hour/ns) Performance: 303.597 0.079 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 12 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.001 96.7 (ns/day) (hour/ns) Performance: 1062.904 0.023 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (117 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.005 0.005 98.5 (ns/day) (hour/ns) Performance: 272.556 0.088 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.002 96.6 (ns/day) (hour/ns) Performance: 974.932 0.025 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (138 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.005 0.005 98.4 (ns/day) (hour/ns) Performance: 268.904 0.089 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 12 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.002 96.6 (ns/day) (hour/ns) Performance: 971.856 0.025 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (142 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.005 0.005 98.4 (ns/day) (hour/ns) Performance: 270.036 0.089 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.002 96.5 (ns/day) (hour/ns) Performance: 975.086 0.025 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (147 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.006 0.006 98.5 (ns/day) (hour/ns) Performance: 257.798 0.093 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.002 96.5 (ns/day) (hour/ns) Performance: 974.161 0.025 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (142 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.005 0.006 98.4 (ns/day) (hour/ns) Performance: 266.565 0.090 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 15 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.002 95.8 (ns/day) (hour/ns) Performance: 954.687 0.025 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (138 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.005 0.005 98.5 (ns/day) (hour/ns) Performance: 286.553 0.084 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 17 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.002 0.002 96.8 (ns/day) (hour/ns) Performance: 926.544 0.026 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (134 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.005 0.006 98.4 (ns/day) (hour/ns) Performance: 263.939 0.091 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.002 96.6 (ns/day) (hour/ns) Performance: 976.632 0.025 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (134 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.005 0.005 98.4 (ns/day) (hour/ns) Performance: 273.379 0.088 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.001 96.6 (ns/day) (hour/ns) Performance: 1048.790 0.023 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (139 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.005 0.006 98.1 (ns/day) (hour/ns) Performance: 262.701 0.091 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.002 96.6 (ns/day) (hour/ns) Performance: 969.409 0.025 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (139 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.006 0.006 98.5 (ns/day) (hour/ns) Performance: 260.744 0.092 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 12 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.001 96.8 (ns/day) (hour/ns) Performance: 1047.008 0.023 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (139 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.006 0.006 98.5 (ns/day) (hour/ns) Performance: 253.429 0.095 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.002 95.6 (ns/day) (hour/ns) Performance: 963.798 0.025 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (140 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.006 0.006 98.5 (ns/day) (hour/ns) Performance: 257.141 0.093 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 12 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.001 96.0 (ns/day) (hour/ns) Performance: 1069.548 0.022 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (133 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.005 0.005 98.3 (ns/day) (hour/ns) Performance: 273.731 0.088 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 12 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.001 96.6 (ns/day) (hour/ns) Performance: 1051.475 0.023 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (133 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.005 0.005 98.5 (ns/day) (hour/ns) Performance: 302.375 0.079 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.001 96.6 (ns/day) (hour/ns) Performance: 1082.896 0.022 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (127 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.006 0.006 98.5 (ns/day) (hour/ns) Performance: 253.023 0.095 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.002 96.6 (ns/day) (hour/ns) Performance: 966.519 0.025 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (140 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.005 0.006 98.4 (ns/day) (hour/ns) Performance: 264.449 0.091 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 17 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.001 97.0 (ns/day) (hour/ns) Performance: 1008.776 0.024 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (139 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.005 0.005 98.6 (ns/day) (hour/ns) Performance: 312.324 0.077 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.002 0.002 96.8 (ns/day) (hour/ns) Performance: 939.831 0.026 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (131 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.006 0.006 98.4 (ns/day) (hour/ns) Performance: 259.711 0.092 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.001 96.7 (ns/day) (hour/ns) Performance: 1034.177 0.023 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (141 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: NVE simulation: will use the initial temperature of 293.480 K for determining the Verlet buffer size Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 5 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 5 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.006 0.006 98.5 (ns/day) (hour/ns) Performance: 255.785 0.094 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21.tpr, VERSION 2019.1 (double precision) Can not increase nstlist because an NVE ensemble is used Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.001 96.8 (ns/day) (hour/ns) Performance: 996.537 0.024 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (137 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.006 0.006 98.3 (ns/day) (hour/ns) Performance: 250.563 0.096 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 14 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.002 96.8 (ns/day) (hour/ns) Performance: 953.357 0.025 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (149 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.006 0.006 98.5 (ns/day) (hour/ns) Performance: 262.399 0.091 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 14 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.002 0.002 96.0 (ns/day) (hour/ns) Performance: 938.829 0.026 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (152 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.004 0.004 98.5 (ns/day) (hour/ns) Performance: 337.641 0.071 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.002 96.7 (ns/day) (hour/ns) Performance: 952.326 0.025 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (144 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.005 0.005 98.5 (ns/day) (hour/ns) Performance: 290.416 0.083 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.002 96.7 (ns/day) (hour/ns) Performance: 961.541 0.025 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (150 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.006 0.006 98.5 (ns/day) (hour/ns) Performance: 260.116 0.092 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 14 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.002 96.7 (ns/day) (hour/ns) Performance: 957.060 0.025 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (157 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.005 0.006 98.5 (ns/day) (hour/ns) Performance: 265.291 0.090 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 14 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.002 96.7 (ns/day) (hour/ns) Performance: 952.620 0.025 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (150 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.005 0.005 98.6 (ns/day) (hour/ns) Performance: 297.039 0.081 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.002 96.6 (ns/day) (hour/ns) Performance: 957.060 0.025 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (145 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.005 0.005 98.4 (ns/day) (hour/ns) Performance: 278.646 0.086 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 14 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.001 96.7 (ns/day) (hour/ns) Performance: 1136.222 0.021 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (145 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.005 0.006 98.5 (ns/day) (hour/ns) Performance: 264.528 0.091 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.001 96.7 (ns/day) (hour/ns) Performance: 1026.252 0.023 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (149 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.005 0.005 98.5 (ns/day) (hour/ns) Performance: 270.795 0.089 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.002 96.7 (ns/day) (hour/ns) Performance: 954.243 0.025 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (150 ms) [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 NOTE 1 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp, line 42]: /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. NOTE 2 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: Setting nstcalcenergy (100) equal to nstenergy (4) Generated 2485 of the 2485 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2485 of the 2485 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'nonanol' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group System is 79.00 Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm Note that mdrun will redetermine rlist based on the actual pair-list setup NOTE 4 [file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 0 Mb of data There were 4 notes Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting mdrun '30 system in water' 16 steps, 0.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 0.005 0.006 98.5 (ns/day) (hour/ns) Performance: 266.681 0.090 Reading file /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32.tpr, VERSION 2019.1 (double precision) Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 Using 1 MPI process Using 1 OpenMP thread NOTE: Thread affinity was not set. starting md rerun '30 system in water', reading coordinates from input trajectory '/dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_normal.trr' Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 NOTE: 13 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s) (%) Time: 0.001 0.002 96.7 (ns/day) (hour/ns) Performance: 960.342 0.025 Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_normal.edr as double precision energy file Opened /dev/shm/gromacs-2019.1/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_rerun.edr as double precision energy file Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (152 ms) [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (4613 ms total) [----------] Global test environment tear-down [==========] 57 tests from 4 test cases ran. (8061 ms total) [ PASSED ] 56 tests. [ FAILED ] 1 test, listed below: [ FAILED ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5, where GetParam() = ("glycine_no_constraints_vacuo", "l-bfgs") 1 FAILED TEST