Log file opened on Wed Jul 23 15:10:37 2014 Host: compute-0-1.local pid: 13596 rank ID: 0 number of ranks: 1 GROMACS: gmx mdrun, VERSION 5.0 (double precision) GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch Gerrit Groenhof Christoph Junghans Peter Kasson Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman 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) 2001-2014, 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 5.0 (double precision) Executable: /home/leontyev/programs/bin/gromacs/gromacs-5.0/bin/gmx_d Library dir: /home/leontyev/programs/bin/gromacs/gromacs-5.0/share/gromacs/top Command line: mdrun_d -nt 1 -s Methylacetamide.tpr -o Methylacetamide.trr -x Methylacetamide.xtc -c Methylacetamide_fin.gro -g Methylacetamide.log Gromacs version: VERSION 5.0 Precision: double Memory model: 64 bit MPI library: thread_mpi OpenMP support: enabled GPU support: disabled invsqrt routine: gmx_software_invsqrt(x) SIMD instructions: AVX_256 FFT library: fftw-3.3.4-sse2-avx RDTSCP usage: enabled C++11 compilation: enabled TNG support: enabled Tracing support: disabled Built on: Fri Jul 18 22:55:04 PDT 2014 Built by: leontyev@cluster01.interxinc.com [CMAKE] Build OS/arch: Linux 2.6.32-431.el6.x86_64 x86_64 Build CPU vendor: GenuineIntel Build CPU brand: Intel(R) Xeon(R) CPU E5-1620 0 @ 3.60GHz Build CPU family: 6 Model: 45 Stepping: 7 Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /export/apps/gcc/4.8.2/bin/gcc-gcc-4.8 GNU 4.8.2 C compiler flags: -mavx -Wno-maybe-uninitialized -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -static-libgcc -static-libstdc++ -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds -O3 -DNDEBUG C++ compiler: /export/apps/gcc/4.8.2/bin/g++-gcc-4.8 GNU 4.8.2 C++ compiler flags: -mavx -std=c++0x -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds -O3 -DNDEBUG Boost version: 1.55.0 (internal) ++++ 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 = 0.001 nsteps = 10 init-step = 0 simulation-part = 1 comm-mode = Linear nstcomm = 103 bd-fric = 0 ld-seed = 4079259596 emtol = 10 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 10000000 nstvout = 10000000 nstfout = 0 nstlog = 1 nstcalcenergy = 100 nstenergy = 100 nstxout-compressed = 0 compressed-x-precision = 1000 cutoff-scheme = Group nstlist = 5 ns-type = Grid pbc = xyz periodic-molecules = FALSE verlet-buffer-tolerance = 0.005 rlist = 1.3 rlistlong = 1.3 nstcalclr = 0 coulombtype = PME coulomb-modifier = None rcoulomb-switch = 1.2 rcoulomb = 1.3 epsilon-r = 1 epsilon-rf = inf vdw-type = Cut-off vdw-modifier = None rvdw-switch = 0 rvdw = 1.3 DispCorr = EnerPres table-extension = 1 fourierspacing = 0.12 fourier-nx = 28 fourier-ny = 28 fourier-nz = 28 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 = Nose-Hoover nsttcouple = 5 nh-chain-length = 1 print-nose-hoover-chain-variables = FALSE pcoupl = Berendsen pcoupltype = Isotropic nstpcouple = 5 tau-p = 5 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]={ 1.01325e+00, 0.00000e+00, 0.00000e+00} ref-p[ 1]={ 0.00000e+00, 1.01325e+00, 0.00000e+00} ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.01325e+00} refcoord-scaling = No 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 = FALSE 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 = no 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 E-x: n = 0 E-xt: n = 0 E-y: n = 0 E-yt: n = 0 E-z: n = 0 E-zt: n = 0 swapcoords = no adress = FALSE userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 grpopts: nrdf: 7125 ref-t: 298.15 tau-t: 1 annealing: No annealing-npoints: 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[ 0]: 0 Using 1 MPI thread Detecting CPU SIMD instructions. Present hardware specification: Vendor: GenuineIntel Brand: Intel(R) Xeon(R) CPU E5-2665 0 @ 2.40GHz Family: 6 Model: 45 Stepping: 7 Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic SIMD instructions most likely to fit this hardware: AVX_256 SIMD instructions selected at GROMACS compile time: AVX_256 NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be removed in a future release when 'verlet' supports all interaction forms. Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE 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 --- -------- -------- Will do ordinary reciprocal space Ewald sum. Using a Gaussian width (1/beta) of 0.416211 nm for Ewald Cut-off's: NS: 1.3 Coulomb: 1.3 LJ: 1.3 Long Range LJ corr.: 7.6923e-04 System total charge: -0.000 Generated table with 4600 data points for Ewald. Tabscale = 2000 points/nm Generated table with 4600 data points for LJ6. Tabscale = 2000 points/nm Generated table with 4600 data points for LJ12. Tabscale = 2000 points/nm Generated table with 4600 data points for 1-4 COUL. Tabscale = 2000 points/nm Generated table with 4600 data points for 1-4 LJ6. Tabscale = 2000 points/nm Generated table with 4600 data points for 1-4 LJ12. Tabscale = 2000 points/nm Potential shift: LJ r^-12: 0.000e+00 r^-6: 0.000e+00, Ewald -0.000e+00 Initialized non-bonded Ewald correction tables, spacing: 1.06e-03 size: 2164 Removing pbc first time Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest There are: 2376 Atoms Max number of connections per atom is 34 Total number of connections is 35640 Max number of graph edges per atom is 4 Total number of graph edges is 4356 Initial temperature: 294.781 K Started mdrun on rank 0 Wed Jul 23 15:10:37 2014 Step Time Lambda 0 0.00000 0.00000 Grid: 3 x 3 x 3 cells Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 2.34312e+03 5.14151e+03 1.33092e+02 3.55685e+03 8.34370e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -1.29147e+04 -3.28852e+03 -1.28735e+02 -1.32510e+03 -2.21748e+03 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -7.86555e+03 8.77660e+03 9.11051e+02 2.96302e+02 -1.32952e+02 Pressure (bar) -1.06735e+03 Step Time Lambda 1 0.00100 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 2.25870e+03 5.08286e+03 1.31952e+02 3.54895e+03 8.29584e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -1.29222e+04 -3.28496e+03 -1.28735e+02 -1.32305e+03 -2.21615e+03 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -8.02299e+03 8.92015e+03 8.97160e+02 3.01148e+02 -1.32952e+02 Pressure (bar) 1.63500e+02 Step Time Lambda 2 0.00200 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 2.18768e+03 4.97970e+03 1.29586e+02 3.53166e+03 8.23951e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -1.29347e+04 -3.28841e+03 -1.28741e+02 -1.31863e+03 -2.21457e+03 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -8.23246e+03 9.11937e+03 8.86912e+02 3.07874e+02 -1.32965e+02 Pressure (bar) 2.07711e+03 Step Time Lambda 3 0.00300 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 2.18880e+03 4.84707e+03 1.26382e+02 3.50555e+03 8.18121e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -1.29476e+04 -3.30159e+03 -1.28741e+02 -1.31679e+03 -2.21362e+03 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -8.42244e+03 9.31325e+03 8.90811e+02 3.14420e+02 -1.32965e+02 Pressure (bar) 4.01299e+03 Step Time Lambda 4 0.00400 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 2.20659e+03 4.70899e+03 1.22781e+02 3.47177e+03 8.13710e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -1.29569e+04 -3.32337e+03 -1.28741e+02 -1.32244e+03 -2.21411e+03 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -8.62169e+03 9.51829e+03 8.96599e+02 3.21342e+02 -1.32965e+02 Pressure (bar) 5.47653e+03 Step Time Lambda 5 0.00500 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 2.16582e+03 4.59404e+03 1.19137e+02 3.43206e+03 8.11586e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -1.29598e+04 -3.34981e+03 -1.28741e+02 -1.33819e+03 -2.21640e+03 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -8.87029e+03 9.75911e+03 8.88816e+02 3.29472e+02 -1.32965e+02 Pressure (bar) 6.16503e+03 Step Time Lambda 6 0.00600 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 2.09465e+03 4.52640e+03 1.15626e+02 3.38857e+03 8.11954e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -1.29565e+04 -3.37629e+03 -1.28741e+02 -1.36332e+03 -2.22027e+03 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -9.10795e+03 9.98096e+03 8.73005e+02 3.36962e+02 -1.32965e+02 Pressure (bar) 6.05073e+03 Step Time Lambda 7 0.00700 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 2.09536e+03 4.51630e+03 1.12242e+02 3.34337e+03 8.12749e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -1.29487e+04 -3.40256e+03 -1.28706e+02 -1.39359e+03 -2.22488e+03 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -9.21845e+03 1.00881e+04 8.69608e+02 3.40578e+02 -1.32891e+02 Pressure (bar) 5.22124e+03 Step Time Lambda 8 0.00800 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 2.18729e+03 4.55616e+03 1.08875e+02 3.29815e+03 8.16690e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -1.29436e+04 -3.42482e+03 -1.28706e+02 -1.42328e+03 -2.22920e+03 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -9.18240e+03 1.00699e+04 8.87536e+02 3.39966e+02 -1.32891e+02 Pressure (bar) 4.56883e+03 Step Time Lambda 9 0.00900 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 2.26212e+03 4.62521e+03 1.05429e+02 3.25408e+03 8.21330e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -1.29445e+04 -3.44812e+03 -1.28706e+02 -1.44546e+03 -2.23212e+03 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -9.13067e+03 1.00356e+04 9.04910e+02 3.38806e+02 -1.32891e+02 Pressure (bar) 4.49459e+03 Step Time Lambda 10 0.01000 0.00000 Writing checkpoint, step 10 at Wed Jul 23 15:10:37 2014 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 2.21648e+03 4.69922e+03 1.01927e+02 3.21190e+03 8.26075e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -1.29541e+04 -3.47543e+03 -1.28706e+02 -1.45550e+03 -2.23304e+03 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -9.19120e+03 1.00913e+04 9.00066e+02 3.40686e+02 -1.32891e+02 Pressure (bar) 5.34039e+03 <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> Statistics over 11 steps using 11 frames Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 2.20060e+03 4.75250e+03 1.18821e+02 3.41299e+03 8.20011e+02 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -1.29439e+04 -3.36035e+03 -1.28727e+02 -1.36594e+03 -2.22108e+03 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -8.71510e+03 9.60660e+03 8.91498e+02 3.24323e+02 -1.32936e+02 Pressure (bar) 3.86396e+03 Box-X Box-Y Box-Z 3.18007e+00 3.18007e+00 3.18007e+00 Total Virial (kJ/mol) -6.14293e+02 -2.49406e+02 -2.10495e+02 -2.49406e+02 -7.39892e+02 -5.44235e+02 -2.10495e+02 -5.44235e+02 -2.64323e+02 Pressure (bar) 4.06644e+03 3.07847e+02 3.03916e+02 3.07847e+02 3.96556e+03 4.76728e+02 3.03916e+02 4.76728e+02 3.55988e+03 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 ----------------------------------------------------------------------------- NB Elec. [V&F] 66.822288 66.822 11.6 NB VdW & Elec. [V&F] 416.214936 416.215 72.4 1,4 nonbonded interactions 0.034848 3.136 0.5 Calc Weights 0.078408 2.823 0.5 Spread Q Bspline 1.672704 3.345 0.6 Gather F Bspline 1.672704 10.036 1.7 3D-FFT 6.965046 55.720 9.7 Solve PME 0.008624 0.552 0.1 NS-Pairs 0.066219 1.391 0.2 Reset In Box 0.000594 0.002 0.0 Shift-X 0.052272 0.314 0.1 CG-CoM 0.007128 0.021 0.0 Bonds 0.023958 1.414 0.2 Angles 0.039204 6.586 1.1 Propers 0.004356 0.998 0.2 RB-Dihedrals 0.015246 3.766 0.7 Virial 0.026631 0.479 0.1 Stop-CM 0.004752 0.048 0.0 P-Coupling 0.026136 0.157 0.0 Calc-Ekin 0.028512 0.770 0.1 ----------------------------------------------------------------------------- Total 574.594 100.0 ----------------------------------------------------------------------------- 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 1 MPI rank Computing: Num Num Call Wall time Giga-Cycles Ranks Threads Count (s) total sum % ----------------------------------------------------------------------------- Neighbor search 1 1 3 0.018 0.043 8.2 Force 1 1 11 0.167 0.402 76.4 PME mesh 1 1 11 0.012 0.029 5.5 Write traj. 1 1 2 0.020 0.047 9.0 Update 1 1 11 0.001 0.002 0.3 Rest 0.001 0.003 0.6 ----------------------------------------------------------------------------- Total 0.219 0.526 100.0 ----------------------------------------------------------------------------- Breakdown of PME mesh computation ----------------------------------------------------------------------------- PME spread/gather 1 1 22 0.005 0.012 2.3 PME 3D-FFT 1 1 22 0.004 0.009 1.7 PME solve Elec 1 1 11 0.003 0.008 1.4 ----------------------------------------------------------------------------- Core t (s) Wall t (s) (%) Time: 0.207 0.219 94.8 (ns/day) (hour/ns) Performance: 4.344 5.525 Finished mdrun on rank 0 Wed Jul 23 15:10:37 2014