Log file opened on Mon Mar 3 18:47:11 2014 Host: md74 pid: 32460 nodeid: 0 nnodes: 1 Gromacs version: VERSION 4.6.5 Precision: single Memory model: 64 bit MPI library: thread_mpi OpenMP support: enabled GPU support: disabled invsqrt routine: gmx_software_invsqrt(x) CPU acceleration: SSE4.1 FFT library: fftw-3.3.2-sse2 Large file support: enabled RDTSCP usage: enabled Built on: Wed Dec 4 12:18:58 CET 2013 Built by: root@md74 [CMAKE] Build OS/arch: Linux 3.5.0-30-generic x86_64 Build CPU vendor: GenuineIntel Build CPU brand: Intel(R) Core(TM) i7 CPU 950 @ 3.07GHz Build CPU family: 6 Model: 26 Stepping: 5 Build CPU features: apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 C compiler: /usr/bin/gcc GNU gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 C compiler flags: -msse4.1 -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG :-) G R O M A C S (-: Gravel Rubs Often Many Awfully Cauterized Sores :-) VERSION 4.6.5 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2012,2013, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program 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. :-) mdrun (-: ++++ 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 = sd nsteps = 10000 init-step = 0 cutoff-scheme = Group ns_type = Grid nstlist = 10 ndelta = 2 nstcomm = 10 comm-mode = Angular nstlog = 1000 nstxout = 1000 nstvout = 1000 nstfout = 0 nstcalcenergy = 10 nstenergy = 10 nstxtcout = 100 init-t = 0 delta-t = 0.001 xtcprec = 1000 fourierspacing = 0.12 nkx = 0 nky = 0 nkz = 0 pme-order = 4 ewald-rtol = 1e-05 ewald-geometry = 0 epsilon-surface = 0 optimize-fft = FALSE ePBC = no bPeriodicMols = FALSE bContinuation = FALSE bShakeSOR = FALSE etc = No bPrintNHChains = FALSE nsttcouple = -1 epc = No epctype = Isotropic nstpcouple = -1 tau-p = 1 ref-p (3x3): ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compress (3x3): compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+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 verlet-buffer-drift = 0.005 rlist = 1 rlistlong = 1 nstcalclr = 0 rtpi = 0.05 coulombtype = Cut-off coulomb-modifier = None rcoulomb-switch = 0 rcoulomb = 1 vdwtype = Cut-off vdw-modifier = None rvdw-switch = 0 rvdw = 1 epsilon-r = 1 epsilon-rf = 1 tabext = 1 implicit-solvent = No gb-algorithm = Still gb-epsilon-solvent = 80 nstgbradii = 1 rgbradii = 1 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 DispCorr = No bSimTemp = FALSE free-energy = no nwall = 0 wall-type = 9-3 wall-atomtype[0] = -1 wall-atomtype[1] = -1 wall-density[0] = 0 wall-density[1] = 0 wall-ewald-zfac = 3 pull = no rotation = FALSE disre = No disre-weighting = Conservative disre-mixed = FALSE dr-fc = 1000 dr-tau = 0 nstdisreout = 100 orires-fc = 0 orires-tau = 0 nstorireout = 100 dihre-fc = 0 em-stepsize = 0.01 em-tol = 10 niter = 20 fc-stepsize = 0 nstcgsteep = 100 nbfgscorr = 10 ConstAlg = Lincs shake-tol = 0.0001 lincs-order = 4 lincs-warnangle = 30 lincs-iter = 1 bd-fric = 0 ld-seed = 1993 cos-accel = 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} adress = FALSE userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 grpopts: nrdf: 174 ref-t: 298 tau-t: 0.1 anneal: No ann-npoints: 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[ 0]: 0 efield-x: n = 0 efield-xt: n = 0 efield-y: n = 0 efield-yt: n = 0 efield-z: n = 0 efield-zt: n = 0 bQMMM = FALSE QMconstraints = 0 QMMMscheme = 0 scalefactor = 1 qm-opts: ngQM = 0 Using 1 MPI thread Detecting CPU-specific acceleration. Present hardware specification: Vendor: GenuineIntel Brand: Intel(R) Core(TM) i7 CPU 950 @ 3.07GHz Family: 6 Model: 26 Stepping: 5 Features: apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 Acceleration most likely to fit this hardware: SSE4.1 Acceleration selected at GROMACS compile time: SSE4.1 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 1 Coulomb: 1 LJ: 1 System total charge: -0.000 Generated table with 1000 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1000 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1000 data points for 1-4 LJ12. Tabscale = 500 points/nm Potential shift: LJ r^-12: 0.000 r^-6 0.000, Coulomb 0.000 Center of mass motion removal mode is Angular We have the following groups for center of mass motion removal: 0: rest There are: 60 Atoms There are: 8 VSites Initial temperature: 0 K Started mdrun on node 0 Mon Mar 3 18:47:11 2014 Step Time Lambda 0 0.00000 0.00000 Grid: 3 x 2 x 2 cells Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 2.04791e+02 1.20127e+02 2.09983e-02 4.01597e+01 1.37061e+02 Coulomb-14 LJ (SR) Coulomb (SR) Potential Kinetic En. 4.00149e+02 2.36433e+02 -7.47544e+02 3.91198e+02 3.63137e+01 Total Energy Temperature Pressure (bar) 4.27512e+02 5.02012e+01 0.00000e+00 Step Time Lambda 1000 1.00000 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 7.56775e+01 1.23640e+02 8.34807e+00 4.85731e+01 7.24606e+01 Coulomb-14 LJ (SR) Coulomb (SR) Potential Kinetic En. 4.26868e+02 -2.64312e+01 -7.86306e+02 -5.71700e+01 2.08900e+02 Total Energy Temperature Pressure (bar) 1.51730e+02 2.88791e+02 0.00000e+00 Step Time Lambda 2000 2.00000 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 1.09065e+02 1.00661e+02 9.27824e+00 7.27224e+01 6.78402e+01 Coulomb-14 LJ (SR) Coulomb (SR) Potential Kinetic En. 4.25549e+02 -2.64317e+01 -7.96226e+02 -3.75420e+01 1.99560e+02 Total Energy Temperature Pressure (bar) 1.62018e+02 2.75879e+02 0.00000e+00 Step Time Lambda 3000 3.00000 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 9.00281e+01 7.31838e+01 3.73827e+00 7.95189e+01 6.30130e+01 Coulomb-14 LJ (SR) Coulomb (SR) Potential Kinetic En. 4.12353e+02 -2.59105e+01 -7.83128e+02 -8.72032e+01 2.12260e+02 Total Energy Temperature Pressure (bar) 1.25057e+02 2.93435e+02 0.00000e+00 Step Time Lambda 4000 4.00000 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 1.13890e+02 1.25285e+02 5.51267e+00 5.76293e+01 4.50904e+01 Coulomb-14 LJ (SR) Coulomb (SR) Potential Kinetic En. 4.13035e+02 -2.33853e+01 -7.89792e+02 -5.27347e+01 2.33597e+02 Total Energy Temperature Pressure (bar) 1.80862e+02 3.22932e+02 0.00000e+00 Step Time Lambda 5000 5.00000 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 1.05341e+02 1.11168e+02 2.84890e+00 6.81440e+01 5.19465e+01 Coulomb-14 LJ (SR) Coulomb (SR) Potential Kinetic En. 4.31300e+02 -3.66114e+01 -7.89405e+02 -5.52676e+01 2.34346e+02 Total Energy Temperature Pressure (bar) 1.79078e+02 3.23968e+02 0.00000e+00 Step Time Lambda 6000 6.00000 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 9.18150e+01 1.39719e+02 3.87641e+00 7.18033e+01 5.04271e+01 Coulomb-14 LJ (SR) Coulomb (SR) Potential Kinetic En. 4.45300e+02 -4.12217e+01 -8.01766e+02 -4.00464e+01 1.94921e+02 Total Energy Temperature Pressure (bar) 1.54875e+02 2.69466e+02 0.00000e+00 Step Time Lambda 7000 7.00000 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 8.82514e+01 1.49453e+02 6.37857e+00 6.46953e+01 6.39850e+01 Coulomb-14 LJ (SR) Coulomb (SR) Potential Kinetic En. 4.37908e+02 -3.13320e+01 -8.09643e+02 -3.03038e+01 2.64560e+02 Total Energy Temperature Pressure (bar) 2.34256e+02 3.65737e+02 0.00000e+00 Step Time Lambda 8000 8.00000 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 1.02398e+02 8.62510e+01 4.40384e+00 6.76715e+01 6.32006e+01 Coulomb-14 LJ (SR) Coulomb (SR) Potential Kinetic En. 4.18371e+02 -2.26227e+01 -7.78243e+02 -5.85707e+01 1.95503e+02 Total Energy Temperature Pressure (bar) 1.36932e+02 2.70269e+02 0.00000e+00 Step Time Lambda 9000 9.00000 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 7.33768e+01 1.42331e+02 4.72449e+00 5.91503e+01 4.92421e+01 Coulomb-14 LJ (SR) Coulomb (SR) Potential Kinetic En. 4.20915e+02 -2.75751e+01 -8.09576e+02 -8.74115e+01 1.94051e+02 Total Energy Temperature Pressure (bar) 1.06639e+02 2.68262e+02 0.00000e+00 Step Time Lambda 10000 10.00000 0.00000 Writing checkpoint, step 10000 at Mon Mar 3 18:47:12 2014 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 8.37332e+01 1.50157e+02 4.61665e+00 5.56212e+01 5.82718e+01 Coulomb-14 LJ (SR) Coulomb (SR) Potential Kinetic En. 4.16016e+02 -3.30250e+01 -7.70338e+02 -3.49468e+01 2.28292e+02 Total Energy Temperature Pressure (bar) 1.93346e+02 3.15599e+02 0.00000e+00 <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> Statistics over 10001 steps using 1001 frames Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 8.49476e+01 1.17149e+02 5.52603e+00 6.51293e+01 6.21664e+01 Coulomb-14 LJ (SR) Coulomb (SR) Potential Kinetic En. 4.27478e+02 -2.85896e+01 -7.93580e+02 -5.97736e+01 2.20303e+02 Total Energy Temperature Pressure (bar) 1.60529e+02 3.04554e+02 0.00000e+00 Total Virial (kJ/mol) 7.56172e+01 1.54175e+00 3.41564e+00 1.54174e+00 8.03665e+01 -3.49566e-01 3.41565e+00 -3.49570e-01 6.15677e+01 Pressure (bar) 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 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] 9.110832 9.111 0.7 NB Elec. [F] 78.619194 78.619 6.4 NB VdW & Elec. [V&F] 51.846425 51.846 4.2 NB VdW & Elec. [F] 395.892504 395.893 32.4 1,4 nonbonded interactions 1.450145 130.513 10.7 NS-Pairs 0.378378 7.946 0.7 CG-CoM 0.068068 0.204 0.0 Bonds 0.590059 34.813 2.8 Angles 1.080108 181.458 14.9 Propers 0.080008 18.322 1.5 RB-Dihedrals 1.120112 276.668 22.6 Virial 0.113113 2.036 0.2 Update 0.680068 21.082 1.7 Stop-CM 0.068136 0.681 0.1 Calc-Ekin 0.136136 3.676 0.3 Virtual Site N 0.600060 9.001 0.7 ----------------------------------------------------------------------------- Total 1221.869 100.0 ----------------------------------------------------------------------------- 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 Computing: Nodes Th. Count Wall t (s) G-Cycles % ----------------------------------------------------------------------------- Vsite constr. 1 1 10001 0.014 0.042 1.2 Neighbor search 1 1 1001 0.052 0.163 4.7 Force 1 1 10001 0.726 2.259 64.7 Vsite spread 1 1 10001 0.014 0.045 1.3 Write traj. 1 1 101 0.028 0.087 2.5 Update 1 1 10001 0.119 0.370 10.6 Rest 1 0.168 0.524 15.0 ----------------------------------------------------------------------------- Total 1 1.122 3.490 100.0 ----------------------------------------------------------------------------- Core t (s) Wall t (s) (%) Time: 1.100 1.122 98.1 (ns/day) (hour/ns) Performance: 770.363 0.031 Finished mdrun on node 0 Mon Mar 3 18:47:12 2014