Log file opened on Fri Mar 22 09:18:11 2019 Host: r2c01cn3.leibniz pid: 11618 rank ID: 0 number of ranks: 112 :-) GROMACS - gmx mdrun, 2018.3 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2017, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2018.3 Executable: /apps/broadwell/centos7/GROMACS/2018.3-intel-2018b-UArecipe/bin/gmx_mpi Data prefix: /apps/broadwell/centos7/GROMACS/2018.3-intel-2018b-UArecipe Working dir: /scratch/gromacs-2019/test2018 Command line: gmx_mpi mdrun -ntomp 1 -s 0519.tpr -o /scratch/gromacs-2019/test2018/0519.trr -x /scratch/gromacs-2019/test2018/0519.xtc -cpo /scratch/gromacs-2019/test2018/0519.cpt -c /scratch/gromacs-2019/test2018/0519.gro -e /scratch/gromacs-2019/test2018/0519.edr -dhdl /scratch/gromacs-2019/test2018/0519.xvg -g /scratch/gromacs-2019/test2018/0519.log -px /scratch/gromacs-2019/test2018/0519.x.xvg -pf /scratch/gromacs-2019/test2018/0519.f.xvg -noconfout -rcon 0.7 -pin on -dds 0.9 -dlb auto -maxh 1 GROMACS version: 2018.3 Precision: single Memory model: 64 bit MPI library: MPI OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support: disabled SIMD instructions: AVX2_256 FFT library: Intel MKL RDTSCP usage: enabled TNG support: enabled Hwloc support: hwloc-1.11.2 Tracing support: disabled Built on: 2018-09-03 09:39:43 Built by: ...@r2c10cn3.leibniz [CMAKE] Build OS/arch: Linux 3.10.0-693.17.1.el7.x86_64 x86_64 Build CPU vendor: Intel Build CPU brand: Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz Build CPU family: 6 Model: 79 Stepping: 1 Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /apps/noarch/intel-psxe/2018_update3/compilers_and_libraries_2018.3.222/linux/mpi/intel64/bin/mpiicc Intel 18.0.3.20180410 C compiler flags: -march=core-avx2 -mkl=sequential -std=gnu99 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits C++ compiler: /apps/noarch/intel-psxe/2018_update3/compilers_and_libraries_2018.3.222/linux/mpi/intel64/bin/mpiicpc Intel 18.0.3.20180410 C++ compiler flags: -march=core-avx2 -mkl=sequential -std=c++11 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits Running on 4 nodes with total 112 cores, 112 logical cores Cores per node: 28 Logical cores per node: 28 Hardware detected on host r2c01cn3.leibniz (the node of MPI rank 0): CPU info: Vendor: Intel Brand: Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz Family: 6 Model: 79 Stepping: 1 Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic Hardware topology: Full, with devices Sockets, cores, and logical processors: Socket 0: [ 0] [ 1] [ 2] [ 3] [ 4] [ 5] [ 6] [ 7] [ 8] [ 9] [ 10] [ 11] [ 12] [ 13] Socket 1: [ 14] [ 15] [ 16] [ 17] [ 18] [ 19] [ 20] [ 21] [ 22] [ 23] [ 24] [ 25] [ 26] [ 27] Numa nodes: Node 0 (68600541184 bytes mem): 0 1 2 3 4 5 6 7 8 9 10 11 12 13 Node 1 (68719476736 bytes mem): 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Latency: 0 1 0 1.00 2.10 1 2.10 1.00 Caches: L1: 32768 bytes, linesize 64 bytes, assoc. 8, shared 1 ways L2: 262144 bytes, linesize 64 bytes, assoc. 8, shared 1 ways L3: 36700160 bytes, linesize 64 bytes, assoc. 20, shared 14 ways PCI devices: 0000:01:00.0 Id: 8086:1521 Class: 0x0200 Numa: 0 0000:01:00.1 Id: 8086:1521 Class: 0x0200 Numa: 0 0000:02:00.0 Id: 15b3:1013 Class: 0x0207 Numa: 0 0000:00:11.4 Id: 8086:8d62 Class: 0x0106 Numa: 0 0000:07:00.0 Id: 1a03:2000 Class: 0x0300 Numa: 0 0000:00:1f.2 Id: 8086:8d02 Class: 0x0106 Numa: 0 ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E. Lindahl GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers SoftwareX 1 (2015) pp. 19-25 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit Bioinformatics 29 (2013) pp. 845-54 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 435-447 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen GROMACS: Fast, Flexible and Free J. Comp. Chem. 26 (2005) pp. 1701-1719 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ E. Lindahl and B. Hess and D. van der Spoel GROMACS 3.0: A package for molecular simulation and trajectory analysis J. Mol. Mod. 7 (2001) pp. 306-317 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ H. J. C. Berendsen, D. van der Spoel and R. van Drunen GROMACS: A message-passing parallel molecular dynamics implementation Comp. Phys. Comm. 91 (1995) pp. 43-56 -------- -------- --- Thank You --- -------- -------- Input Parameters: integrator = md tinit = 0 dt = 0.002 nsteps = 500000 init-step = 0 simulation-part = 1 comm-mode = Linear nstcomm = 100 bd-fric = 0 ld-seed = -350048814 emtol = 10 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 50000 nstcalcenergy = 100 nstenergy = 50000 nstxout-compressed = 50000 compressed-x-precision = 1000 cutoff-scheme = Verlet nstlist = 20 ns-type = Grid pbc = xyz periodic-molecules = false verlet-buffer-tolerance = 0.005 rlist = 1.223 coulombtype = PME coulomb-modifier = Potential-shift rcoulomb-switch = 0 rcoulomb = 1.2 epsilon-r = 1 epsilon-rf = inf vdw-type = Cut-off vdw-modifier = Potential-shift rvdw-switch = 1 rvdw = 1.2 DispCorr = EnerPres table-extension = 1 fourierspacing = 0.16 fourier-nx = 96 fourier-ny = 84 fourier-nz = 80 pme-order = 4 ewald-rtol = 1e-05 ewald-rtol-lj = 0.001 lj-pme-comb-rule = Geometric ewald-geometry = 0 epsilon-surface = 0 implicit-solvent = No gb-algorithm = Still nstgbradii = 1 rgbradii = 1 gb-epsilon-solvent = 80 gb-saltconc = 0 gb-obc-alpha = 1 gb-obc-beta = 0.8 gb-obc-gamma = 4.85 gb-dielectric-offset = 0.009 sa-algorithm = Ace-approximation sa-surface-tension = 2.05016 tcoupl = V-rescale nsttcouple = 20 nh-chain-length = 0 print-nose-hoover-chain-variables = false pcoupl = Berendsen pcoupltype = Isotropic nstpcouple = 20 tau-p = 2 compressibility (3x3): compressibility[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00} compressibility[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00} compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05} ref-p (3x3): ref-p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00} ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00} refcoord-scaling = COM posres-com (3): posres-com[0]= 0.00000e+00 posres-com[1]= 0.00000e+00 posres-com[2]= 0.00000e+00 posres-comB (3): posres-comB[0]= 0.00000e+00 posres-comB[1]= 0.00000e+00 posres-comB[2]= 0.00000e+00 QMMM = false QMconstraints = 0 QMMMscheme = 0 MMChargeScaleFactor = 1 qm-opts: ngQM = 0 constraint-algorithm = Lincs continuation = true Shake-SOR = false shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 nwall = 0 wall-type = 9-3 wall-r-linpot = -1 wall-atomtype[0] = -1 wall-atomtype[1] = -1 wall-density[0] = 0 wall-density[1] = 0 wall-ewald-zfac = 3 pull = true pull-cylinder-r = 1.5 pull-constr-tol = 1e-06 pull-print-COM = true pull-print-ref-value = true pull-print-components = true pull-nstxout = 50000 pull-nstfout = 50000 pull-ngroups = 3 pull-group 0: atom: not available weight: not available pbcatom = -1 pull-group 1: atom (1): atom[0]=1442 weight: not available pbcatom = -1 pull-group 2: atom (2): atom[0]=4641 atom[1]=4643 weight: not available pbcatom = 4641 pull-ncoords = 1 pull-coord 0: type = umbrella geometry = distance group[0] = 1 group[1] = 2 dim (3): dim[0]=1 dim[1]=1 dim[2]=1 origin (3): origin[0]= 0.00000e+00 origin[1]= 0.00000e+00 origin[2]= 0.00000e+00 vec (3): vec[0]= 0.00000e+00 vec[1]= 0.00000e+00 vec[2]= 0.00000e+00 start = true init = 0.518654 rate = 0 k = 1000 kB = 1000 awh = false rotation = false interactiveMD = false disre = No disre-weighting = Conservative disre-mixed = false dr-fc = 1000 dr-tau = 0 nstdisreout = 100 orire-fc = 0 orire-tau = 0 nstorireout = 100 free-energy = no cos-acceleration = 0 deform (3x3): deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} simulated-tempering = false swapcoords = no userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 applied-forces: electric-field: x: E0 = 0 omega = 0 t0 = 0 sigma = 0 y: E0 = 0 omega = 0 t0 = 0 sigma = 0 z: E0 = 0 omega = 0 t0 = 0 sigma = 0 grpopts: nrdf: 12909.9 439152 ref-t: 300 300 tau-t: 0.1 0.1 annealing: No No annealing-npoints: 0 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[ 0]: 0 Changing nstlist from 20 to 80, rlist from 1.223 to 1.326 Initializing Domain Decomposition on 112 ranks Dynamic load balancing: locked Minimum cell size due to atom displacement: 0.625 nm Initial maximum inter charge-group distances: two-body bonded interactions: 0.443 nm, LJ-14, atoms 1990 2780 multi-body bonded interactions: 0.443 nm, Proper Dih., atoms 1990 2780 Minimum cell size due to bonded interactions: 0.487 nm User supplied maximum distance required for P-LINCS: 0.700 nm Guess for relative PME load: 0.13 Will use 96 particle-particle and 16 PME only ranks This is a guess, check the performance at the end of the log file Using 16 separate PME ranks, as guessed by mdrun Scaling the initial minimum size with 1/0.9 (option -dds) = 1.11111 Optimizing the DD grid for 96 cells with a minimum initial size of 0.778 nm The maximum allowed number of cells is: X 18 Y 17 Z 15 Domain decomposition grid 4 x 4 x 6, separate PME ranks 16 PME domain decomposition: 4 x 4 x 1 Interleaving PP and PME ranks This rank does only particle-particle work. Domain decomposition rank 0, coordinates 0 0 0 The initial number of communication pulses is: X 1 Y 1 Z 1 The initial domain decomposition cell size is: X 3.63 nm Y 3.31 nm Z 2.00 nm The maximum allowed distance for charge groups involved in interactions is: non-bonded interactions 1.326 nm (the following are initial values, they could change due to box deformation) two-body bonded interactions (-rdd) 1.326 nm multi-body bonded interactions (-rdd) 1.326 nm atoms separated by up to 5 constraints (-rcon) 2.003 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 1 Y 1 Z 1 The minimum size for domain decomposition cells is 1.326 nm The requested allowed shrink of DD cells (option -dds) is: 0.90 The allowed shrink of domain decomposition cells is: X 0.37 Y 0.40 Z 0.66 The maximum allowed distance for charge groups involved in interactions is: non-bonded interactions 1.326 nm two-body bonded interactions (-rdd) 1.326 nm multi-body bonded interactions (-rdd) 1.326 nm atoms separated by up to 5 constraints (-rcon) 1.326 nm Using two step summing over 4 groups of on average 24.0 ranks Using 112 MPI processes Using 1 OpenMP thread per MPI process Overriding thread affinity set outside gmx mdrun Pinning threads with an auto-selected logical core stride of 1 System total charge: -0.000 Will do PME sum in reciprocal space for electrostatic interactions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 103 (1995) pp. 8577-8592 -------- -------- --- Thank You --- -------- -------- Using a Gaussian width (1/beta) of 0.384195 nm for Ewald Potential shift: LJ r^-12: -1.122e-01 r^-6: -3.349e-01, Ewald -8.333e-06 Initialized non-bonded Ewald correction tables, spacing: 1.02e-03 size: 1176 Long Range LJ corr.: 3.1361e-04 Generated table with 1163 data points for Ewald. Tabscale = 500 points/nm Generated table with 1163 data points for LJ6. Tabscale = 500 points/nm Generated table with 1163 data points for LJ12. Tabscale = 500 points/nm Generated table with 1163 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1163 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1163 data points for 1-4 LJ12. Tabscale = 500 points/nm Using SIMD 4x8 nonbonded short-range kernels Using a dual 4x8 pair-list setup updated with dynamic pruning: outer list: updated every 80 steps, buffer 0.126 nm, rlist 1.326 nm inner list: updated every 13 steps, buffer 0.002 nm, rlist 1.202 nm At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: outer list: updated every 80 steps, buffer 0.275 nm, rlist 1.475 nm inner list: updated every 13 steps, buffer 0.052 nm, rlist 1.252 nm Using full Lennard-Jones parameter combination matrix Will apply potential COM pulling with 1 pull coordinate and 2 groups Pull group 1: 1 atoms, mass 13.019 Pull group 2: 2 atoms, mass 26.018 Will use a sub-communicator for pull communication Initializing Parallel LINear Constraint Solver ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess P-LINCS: A Parallel Linear Constraint Solver for molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 116-122 -------- -------- --- Thank You --- -------- -------- The number of constraints is 1073 There are inter charge-group constraints, will communicate selected coordinates each lincs iteration ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ S. Miyamoto and P. A. Kollman SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models J. Comp. Chem. 13 (1992) pp. 952-962 -------- -------- --- Thank You --- -------- -------- Linking all bonded interactions to atoms The -noconfout functionality is deprecated, and may be removed in a future version. Intra-simulation communication will occur every 20 steps. Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ G. Bussi, D. Donadio and M. Parrinello Canonical sampling through velocity rescaling J. Chem. Phys. 126 (2007) pp. 014101 -------- -------- --- Thank You --- -------- -------- There are: 224238 Atoms Atom distribution over 96 domains: av 2335 stddev 86 min 2090 max 2430 Started mdrun on rank 0 Fri Mar 22 09:18:14 2019 Step Time 0 0.00000 Energies (kJ/mol) G96Bond G96Angle Proper Dih. Improper Dih. LJ-14 5.09960e+03 7.77425e+03 4.85656e+03 2.47900e+03 -1.61705e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 6.64263e+04 5.11422e+05 -1.65591e+04 -3.68724e+06 1.05264e+04 COM Pull En. Potential Kinetic En. Total Energy Conserved En. 6.82855e-14 -3.09538e+06 9.65238e+03 -3.08573e+06 -3.08550e+06 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 5.13609e+00 -1.19286e+02 -1.38954e+03 2.44671e-06 DD step 79 load imb.: force 4.9% pme mesh/force 0.852 step 240 Turning on dynamic load balancing, because the performance loss due to load imbalance is 3.8 %. step 8000 Turning off dynamic load balancing, because it is degrading performance. Atom distribution over 96 domains: av 2335 stddev 86 min 2110 max 2401 step 24000 Turning on dynamic load balancing, because the performance loss due to load imbalance is 6.7 %. step 25600 Turning off dynamic load balancing, because it is degrading performance. Atom distribution over 96 domains: av 2335 stddev 89 min 2078 max 2408 step 32000 Turning on dynamic load balancing, because the performance loss due to load imbalance is 6.0 %. step 35200 Turning off dynamic load balancing, because it is degrading performance. Atom distribution over 96 domains: av 2335 stddev 87 min 2092 max 2408 step 40000 Will no longer try dynamic load balancing, as it degraded performance. DD step 49999 load imb.: force 5.3% pme mesh/force 0.644 Step Time 50000 100.00000 Energies (kJ/mol) G96Bond G96Angle Proper Dih. Improper Dih. LJ-14 4.83032e+03 7.91144e+03 4.75862e+03 2.58501e+03 -1.28384e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 6.65623e+04 5.12972e+05 -1.65428e+04 -3.69199e+06 1.06877e+04 COM Pull En. Potential Kinetic En. Total Energy Conserved En. 3.75102e+00 -3.09835e+06 5.63326e+05 -2.53502e+06 -3.10342e+06 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 2.99749e+02 -1.19052e+02 -1.98544e+00 2.95643e-06 DD step 99999 load imb.: force 5.7% pme mesh/force 0.647 Step Time 100000 200.00000 Energies (kJ/mol) G96Bond G96Angle Proper Dih. Improper Dih. LJ-14 4.75345e+03 7.58282e+03 4.85553e+03 2.57402e+03 -1.79248e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 6.64540e+04 5.11097e+05 -1.65655e+04 -3.68951e+06 1.06834e+04 COM Pull En. Potential Kinetic En. Total Energy Conserved En. 3.31456e+00 -3.09825e+06 5.64329e+05 -2.53392e+06 -3.10198e+06 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 3.00283e+02 -1.19378e+02 -2.32919e+01 2.76256e-06 DD step 149999 load imb.: force 5.5% pme mesh/force 0.641 Step Time 150000 300.00000 Energies (kJ/mol) G96Bond G96Angle Proper Dih. Improper Dih. LJ-14 5.04330e+03 7.84732e+03 4.76267e+03 2.59187e+03 -1.62709e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 6.63614e+04 5.11111e+05 -1.65646e+04 -3.68670e+06 1.05392e+04 COM Pull En. Potential Kinetic En. Total Energy Conserved En. 6.31904e+00 -3.09516e+06 5.63786e+05 -2.53138e+06 -3.10055e+06 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 2.99994e+02 -1.19365e+02 1.36845e+01 2.96967e-06 Writing checkpoint, step 188880 at Fri Mar 22 09:33:14 2019 DD step 199999 load imb.: force 3.8% pme mesh/force 0.657 Step Time 200000 400.00000 Energies (kJ/mol) G96Bond G96Angle Proper Dih. Improper Dih. LJ-14 4.94785e+03 7.55779e+03 4.90840e+03 2.40698e+03 -7.60589e+01 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 6.66943e+04 5.10013e+05 -1.65563e+04 -3.68945e+06 1.06891e+04 COM Pull En. Potential Kinetic En. Total Energy Conserved En. 1.73298e+01 -3.09885e+06 5.65413e+05 -2.53344e+06 -3.09905e+06 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 3.00859e+02 -1.19246e+02 -6.90249e+01 2.82245e-06 DD step 249999 load imb.: force 5.9% pme mesh/force 0.640 Step Time 250000 500.00000 Energies (kJ/mol) G96Bond G96Angle Proper Dih. Improper Dih. LJ-14 5.04615e+03 7.56546e+03 4.92053e+03 2.49466e+03 -1.13046e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 6.66422e+04 5.12506e+05 -1.65587e+04 -3.69014e+06 1.06123e+04 COM Pull En. Potential Kinetic En. Total Energy Conserved En. 1.24707e+01 -3.09701e+06 5.64644e+05 -2.53237e+06 -3.09746e+06 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 3.00450e+02 -1.19281e+02 1.69750e+01 3.14922e-06 DD step 299999 load imb.: force 5.1% pme mesh/force 0.645 Step Time 300000 600.00000 Energies (kJ/mol) G96Bond G96Angle Proper Dih. Improper Dih. LJ-14 4.87397e+03 7.61933e+03 4.95450e+03 2.49306e+03 -1.36325e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 6.64239e+04 5.13536e+05 -1.65692e+04 -3.69342e+06 1.05761e+04 COM Pull En. Potential Kinetic En. Total Energy Conserved En. 1.48148e+01 -3.09963e+06 5.64550e+05 -2.53508e+06 -3.09601e+06 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 3.00400e+02 -1.19431e+02 3.83472e+01 3.14445e-06 DD step 349999 load imb.: force 6.2% pme mesh/force 0.638 Step Time 350000 700.00000 Energies (kJ/mol) G96Bond G96Angle Proper Dih. Improper Dih. LJ-14 5.08991e+03 7.69764e+03 4.89299e+03 2.53503e+03 -1.66483e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 6.63619e+04 5.11430e+05 -1.65514e+04 -3.68938e+06 1.05755e+04 COM Pull En. Potential Kinetic En. Total Energy Conserved En. 9.36988e+00 -3.09751e+06 5.63559e+05 -2.53395e+06 -3.09443e+06 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 2.99873e+02 -1.19176e+02 -4.38299e+01 2.81165e-06 Writing checkpoint, step 377760 at Fri Mar 22 09:48:14 2019 DD step 399999 load imb.: force 5.4% pme mesh/force 0.640 Step Time 400000 800.00000 Energies (kJ/mol) G96Bond G96Angle Proper Dih. Improper Dih. LJ-14 4.83583e+03 7.86137e+03 4.79819e+03 2.54585e+03 -1.37643e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 6.65807e+04 5.13211e+05 -1.65584e+04 -3.69136e+06 1.06535e+04 COM Pull En. Potential Kinetic En. Total Energy Conserved En. 1.91043e+01 -3.09755e+06 5.63681e+05 -2.53387e+06 -3.09296e+06 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 2.99938e+02 -1.19276e+02 7.98090e+00 3.10775e-06 DD step 449999 load imb.: force 3.9% pme mesh/force 0.623 Step Time 450000 900.00000 Energies (kJ/mol) G96Bond G96Angle Proper Dih. Improper Dih. LJ-14 5.03504e+03 7.58068e+03 4.95366e+03 2.55010e+03 -7.27573e+01 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 6.67311e+04 5.10533e+05 -1.65552e+04 -3.68593e+06 1.06144e+04 COM Pull En. Potential Kinetic En. Total Energy Conserved En. 9.14612e+00 -3.09455e+06 5.63459e+05 -2.53109e+06 -3.09145e+06 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 2.99820e+02 -1.19230e+02 2.88342e+00 2.83940e-06 DD step 499999 load imb.: force 5.3% pme mesh/force 0.629 Step Time 500000 1000.00000 Energies (kJ/mol) G96Bond G96Angle Proper Dih. Improper Dih. LJ-14 4.86851e+03 7.78448e+03 5.02171e+03 2.57295e+03 -1.99886e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 6.65664e+04 5.11263e+05 -1.65511e+04 -3.69094e+06 1.05802e+04 COM Pull En. Potential Kinetic En. Total Energy Conserved En. 5.72201e+00 -3.09903e+06 5.61760e+05 -2.53727e+06 -3.08991e+06 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 2.98916e+02 -1.19172e+02 -8.74913e+01 2.84239e-06 <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> Statistics over 500001 steps using 5001 frames Energies (kJ/mol) G96Bond G96Angle Proper Dih. Improper Dih. LJ-14 4.91060e+03 7.67629e+03 4.91081e+03 2.55615e+03 -1.84510e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 6.65040e+04 5.12981e+05 -1.65579e+04 -3.69164e+06 1.05927e+04 COM Pull En. Potential Kinetic En. Total Energy Conserved En. 8.79495e+00 -3.09824e+06 5.63645e+05 -2.53459e+06 -3.09749e+06 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 2.99919e+02 -1.19269e+02 1.04596e+00 0.00000e+00 Box-X Box-Y Box-Z 1.45132e+01 1.32261e+01 1.20182e+01 Total Virial (kJ/mol) 1.87733e+05 1.80507e+01 -5.28405e+01 1.99566e+01 1.87843e+05 1.49384e+01 -5.10672e+01 1.46297e+01 1.87851e+05 Pressure (bar) 2.00325e+00 -4.36769e-01 8.11049e-01 -4.64232e-01 5.17693e-01 -1.78615e-01 7.85505e-01 -1.74166e-01 6.16928e-01 T-protein_and_gpfT-water_and_ions 2.99993e+02 2.99916e+02 M E G A - F L O P S A C C O U N T I N G NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table W3=SPC/TIP3p W4=TIP4p (single or pairs) V&F=Potential and force V=Potential only F=Force only Computing: M-Number M-Flops % Flops ----------------------------------------------------------------------------- Pair Search distance check 845339.861640 7608058.755 0.1 NxN Ewald Elec. + LJ [F] 53531920.679536 3533106764.849 51.0 NxN Ewald Elec. + LJ [V&F] 540836.388816 57869493.603 0.8 NxN LJ [F] 77728.720608 2565047.780 0.0 NxN LJ [V&F] 785.026592 33756.143 0.0 NxN Ewald Elec. [F] 50759238.604624 3096313554.882 44.7 NxN Ewald Elec. [V&F] 512821.787472 43077030.148 0.6 1,4 nonbonded interactions 3669.507339 330255.661 0.0 Calc Weights 336357.672714 12108876.218 0.2 Spread Q Bspline 7175630.351232 14351260.702 0.2 Gather F Bspline 7175630.351232 43053782.107 0.6 3D-FFT 12450329.900610 99602639.205 1.4 Solve PME 16128.032256 1032194.064 0.0 Reset In Box 1400.814786 4202.444 0.0 CG-CoM 1401.711738 4205.135 0.0 Bonds 1849.003698 109091.218 0.0 Angles 3514.507029 590437.181 0.0 Propers 1640.503281 375675.251 0.0 Impropers 1287.002574 267696.535 0.0 Virial 5714.178558 102855.214 0.0 Stop-CM 1121.414238 11214.142 0.0 P-Coupling 5606.174238 33637.045 0.0 Calc-Ekin 11212.348476 302733.409 0.0 Lincs 566.014829 33960.890 0.0 Lincs-Mat 954.342888 3817.372 0.0 Constraint-V 121602.252436 972818.019 0.0 Constraint-Vir 6052.042015 145249.008 0.0 Settle 40156.740926 12970627.319 0.2 ----------------------------------------------------------------------------- Total 6926980934.302 100.0 ----------------------------------------------------------------------------- D O M A I N D E C O M P O S I T I O N S T A T I S T I C S av. #atoms communicated per step for force: 2 x 447044.7 av. #atoms communicated per step for LINCS: 2 x 21812.1 Dynamic load balancing report: DLB got disabled because it was unsuitable to use. Average load imbalance: 7.8%. The balanceable part of the MD step is 87%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 6.7%. Average PME mesh/force load: 0.628 Part of the total run time spent waiting due to PP/PME imbalance: 5.0 % NOTE: 6.7 % of the available CPU time was lost due to load imbalance in the domain decomposition. You might want to use dynamic load balancing (option -dlb.) R E A L C Y C L E A N D T I M E A C C O U N T I N G On 96 MPI ranks doing PP, and on 16 MPI ranks doing PME Computing: Num Num Call Wall time Giga-Cycles Ranks Threads Count (s) total sum % ----------------------------------------------------------------------------- Domain decomp. 96 1 6250 17.190 3960.630 0.6 DD comm. load 96 1 173 0.004 0.867 0.0 DD comm. bounds 96 1 157 0.007 1.726 0.0 Send X to PME 96 1 500001 1.973 454.537 0.1 Neighbor search 96 1 6251 33.463 7709.991 1.2 Comm. coord. 96 1 493750 38.782 8935.419 1.4 Force 96 1 500001 2026.176 466836.010 73.0 Wait + Comm. F 96 1 500001 103.307 23802.143 3.7 PME mesh * 16 1 500001 1402.994 53875.529 8.4 PME wait for PP * 976.796 37509.361 5.9 Wait + Recv. PME F 96 1 500001 5.720 1317.844 0.2 NB X/F buffer ops. 96 1 1487501 21.655 4989.357 0.8 COM pull force 96 1 500001 6.986 1609.659 0.3 Write traj. 96 1 13 0.036 8.262 0.0 Update 96 1 500001 5.806 1337.611 0.2 Constraints 96 1 500001 112.219 25855.418 4.0 Comm. energies 96 1 25001 3.201 737.606 0.1 Rest 3.280 755.727 0.1 ----------------------------------------------------------------------------- Total 2379.805 639698.273 100.0 ----------------------------------------------------------------------------- (*) Note that with separate PME ranks, the walltime column actually sums to twice the total reported, but the cycle count total and % are correct. ----------------------------------------------------------------------------- Breakdown of PME mesh computation ----------------------------------------------------------------------------- PME redist. X/F 16 1 1000002 198.588 7625.860 1.2 PME spread 16 1 500001 460.457 17681.751 2.8 PME gather 16 1 500001 289.656 11122.896 1.7 PME 3D-FFT 16 1 1000002 317.011 12173.346 1.9 PME 3D-FFT Comm. 16 1 2000004 107.426 4125.187 0.6 PME solve Elec 16 1 500001 28.890 1109.375 0.2 ----------------------------------------------------------------------------- Core t (s) Wall t (s) (%) Time: 266538.111 2379.805 11200.0 39:39 (ns/day) (hour/ns) Performance: 36.306 0.661 Finished mdrun on rank 0 Fri Mar 22 09:57:54 2019