Log file opened on Tue Nov 3 23:57:24 2009 Host: linux-g11s pid: 7564 nodeid: 0 nnodes: 1 The Gromacs distribution was built Mon Aug 17 21:40:31 EDT 2009 by reza@linux-g11s (Linux 2.6.27.25-0.1-default x86_64) :-) G R O M A C S (-: GROwing Monsters And Cloning Shrimps :-) VERSION 4.0.4 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, 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 General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) /home/reza/gromacs/404/bin/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 = 500 init_step = 0 ns_type = Simple nstlist = 0 ndelta = 2 nstcomm = 0 comm_mode = None nstlog = 100 nstxout = 500 nstvout = 500 nstfout = 0 nstenergy = 50 nstxtcout = 500 init_t = 0 delta_t = 0.002 xtcprec = 10000 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 epc = No epctype = Isotropic 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 andersen_seed = 815131 rlist = 999 rtpi = 0.05 coulombtype = Cut-off rcoulomb_switch = 0 rcoulomb = 999 vdwtype = Cut-off rvdw_switch = 0 rvdw = 999 epsilon_r = 1 epsilon_rf = 1 tabext = 1 implicit_solvent = No gb_algorithm = Still gb_epsilon_solvent = 80 nstgbradii = 1 rgbradii = 2 gb_saltconc = 0 gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 sa_surface_tension = 2.092 DispCorr = No free_energy = no init_lambda = 0 sc_alpha = 0 sc_power = 0 sc_sigma = 0.3 delta_lambda = 0 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 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 = 1000 em_stepsize = 0.01 em_tol = 10 niter = 20 fc_stepsize = 0 nstcgsteep = 1000 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} userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 grpopts: nrdf: 0 ref_t: 298 tau_t: 1 anneal: No ann_npoints: 0 acc: 0 0 0 nfreeze: Y Y Y energygrp_flags[ 0]: 1 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 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 999 Coulomb: 999 LJ: 999 System total charge: 0.000 Configuring nonbonded kernels... Testing x86_64 SSE support... present. There are: 10 Atoms Initial temperature: 0 K Started mdrun on node 0 Tue Nov 3 23:57:24 2009 Step Time Lambda 0 0.00000 0.00000 Energies (kJ/mol) Bond Angle LJ (SR) Coulomb (SR) Potential 1.81765e-03 1.40983e+00 0.00000e+00 0.00000e+00 1.41165e+00 Kinetic En. Total Energy Temperature Pressure (bar) 0.00000e+00 1.41165e+00 0.00000e+00 0.00000e+00 Step Time Lambda 100 0.20000 0.00000 Energies (kJ/mol) Bond Angle LJ (SR) Coulomb (SR) Potential 1.81765e-03 1.40983e+00 0.00000e+00 0.00000e+00 1.41165e+00 Kinetic En. Total Energy Temperature Pressure (bar) 0.00000e+00 1.41165e+00 0.00000e+00 0.00000e+00 Step Time Lambda 200 0.40000 0.00000 Energies (kJ/mol) Bond Angle LJ (SR) Coulomb (SR) Potential 1.81765e-03 1.40983e+00 0.00000e+00 0.00000e+00 1.41165e+00 Kinetic En. Total Energy Temperature Pressure (bar) 0.00000e+00 1.41165e+00 0.00000e+00 0.00000e+00 Step Time Lambda 300 0.60000 0.00000 Energies (kJ/mol) Bond Angle LJ (SR) Coulomb (SR) Potential 1.81765e-03 1.40983e+00 0.00000e+00 0.00000e+00 1.41165e+00 Kinetic En. Total Energy Temperature Pressure (bar) 0.00000e+00 1.41165e+00 0.00000e+00 0.00000e+00 Step Time Lambda 400 0.80000 0.00000 Energies (kJ/mol) Bond Angle LJ (SR) Coulomb (SR) Potential 1.81765e-03 1.40983e+00 0.00000e+00 0.00000e+00 1.41165e+00 Kinetic En. Total Energy Temperature Pressure (bar) 0.00000e+00 1.41165e+00 0.00000e+00 0.00000e+00 Step Time Lambda 500 1.00000 0.00000 Writing checkpoint, step 500 at Tue Nov 3 23:57:24 2009 Energies (kJ/mol) Bond Angle LJ (SR) Coulomb (SR) Potential 1.81765e-03 1.40983e+00 0.00000e+00 0.00000e+00 1.41165e+00 Kinetic En. Total Energy Temperature Pressure (bar) 0.00000e+00 1.41165e+00 0.00000e+00 0.00000e+00 <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> Energies (kJ/mol) Bond Angle LJ (SR) Coulomb (SR) Potential 1.81765e-03 1.40983e+00 0.00000e+00 0.00000e+00 1.41165e+00 Kinetic En. Total Energy Temperature Pressure (bar) 0.00000e+00 1.41165e+00 0.00000e+00 0.00000e+00 Total Virial (kJ/mol) -3.97651e-01 -5.11801e-01 6.04670e-01 -5.11801e-01 -2.00984e+00 -1.65965e-01 6.04669e-01 -1.65965e-01 -9.91479e-02 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 Total Dipole (Debye) 5.76356e-04 5.76363e-04 -5.76391e-04 <====== ############################### ==> <==== R M S - F L U C T U A T I O N S ====> <== ############################### ======> Energies (kJ/mol) Bond Angle LJ (SR) Coulomb (SR) Potential 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 Kinetic En. Total Energy Temperature Pressure (bar) 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 Total Virial (kJ/mol) 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 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 Total Dipole (Debye) 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 RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or pairs) NF=No Forces Computing: M-Number M-Flops % Flops ----------------------------------------------------------------------- NS-Pairs 0.000055 0.001 0.1 CG-CoM 0.000010 0.000 0.0 Bonds 0.004008 0.236 10.8 Angles 0.006012 1.010 46.1 Virial 0.027555 0.496 22.6 Update 0.010020 0.311 14.2 Calc-Ekin 0.005020 0.136 6.2 ----------------------------------------------------------------------- Total 2.190 100.0 ----------------------------------------------------------------------- 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 Number G-Cycles Seconds % ----------------------------------------------------------------------- Neighbor search 1 1 0.000 0.0 2.7 Force 1 501 0.003 0.0 31.0 Write traj. 1 2 0.001 0.0 13.2 Update 1 501 0.001 0.0 12.5 Rest 1 0.004 0.0 40.6 ----------------------------------------------------------------------- Total 1 0.011 0.0 100.0 ----------------------------------------------------------------------- nodetime = 0! Infinite Giga flopses! Finished mdrun on node 0 Tue Nov 3 23:57:24 2009