Log file opened on Tue Oct 14 17:03:18 2008 Host: linux-f29d pid: 4086 nodeid: 0 nnodes: 1 The Gromacs distribution was built Thu Jan 15 22:35:06 MSK 2009 by root@linux-f29d (Linux 2.6.25.5-1.1-default x86_64) :-) G R O M A C S (-: GROwing Monsters And Cloning Shrimps :-) VERSION 4.0.2 (-: 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. :-) 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 = md nsteps = 2500 init_step = 0 ns_type = Grid nstlist = 10 ndelta = 2 nstcomm = 1 comm_mode = Linear nstlog = 100 nstxout = 100 nstvout = 100 nstfout = 0 nstenergy = 100 nstxtcout = 0 init_t = 0 delta_t = 0.002 xtcprec = 1000 nkx = 96 nky = 96 nkz = 96 pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 0 epsilon_surface = 0 optimize_fft = FALSE ePBC = xyz bPeriodicMols = FALSE bContinuation = FALSE bShakeSOR = FALSE etc = Berendsen epc = Berendsen epctype = Isotropic tau_p = 1 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} compress (3x3): compress[ 0]={ 5.00000e-05, 0.00000e+00, 0.00000e+00} compress[ 1]={ 0.00000e+00, 5.00000e-05, 0.00000e+00} compress[ 2]={ 0.00000e+00, 0.00000e+00, 5.00000e-05} 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 = 1 rtpi = 0.05 coulombtype = PME rcoulomb_switch = 0 rcoulomb = 1 vdwtype = Cut-off 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 = 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: 11009.8 178557 ref_t: 298 298 tau_t: 0.1 0.1 anneal: No No ann_npoints: 0 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 Table routines are used for coulomb: TRUE Table routines are used for vdw: FALSE Will do PME sum in reciprocal space. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ U. Essman, L. Perela, 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 0.320163 nm for Ewald Cut-off's: NS: 1 Coulomb: 1 LJ: 1 System total charge: -0.000 Generated table with 1000 data points for Ewald. Tabscale = 500 points/nm Generated table with 1000 data points for LJ6. Tabscale = 500 points/nm Generated table with 1000 data points for LJ12. Tabscale = 500 points/nm 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 Enabling SPC water optimization for 29758 molecules. Configuring nonbonded kernels... Testing x86_64 SSE support... present. Removing pbc first time ++++ 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 --- -------- -------- 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 ++++ H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak Molecular dynamics with coupling to an external bath J. Chem. Phys. 81 (1984) pp. 3684-3690 -------- -------- --- Thank You --- -------- -------- There are: 92948 Atoms Max number of connections per atom is 59 Total number of connections is 201722 Max number of graph edges per atom is 5 Total number of graph edges is 126470 Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (step 0) RMS relative constraint deviation after constraining: 0.00e+00 Initial temperature: 3.74839e-06 K Started mdrun on node 0 Tue Oct 14 17:03:20 2008 Step Time Lambda 0 0.00000 0.00000 Grid: 17 x 17 x 12 cells Large VCM(group rest): -5425561337856.00000, -0.00127, -0.00028, Temp-cm: 1.50471e+27 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 1.80437e+07 5.02577e+04 1.46998e+02 9.81211e+03 1.74070e+14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Position Rest. 4.42124e+04 2.81684e+24 -1.31171e+06 -1.55469e+05 4.73278e-07 Potential Kinetic En. Total Energy Temperature Pressure (bar) 2.81684e+24 inf inf inf inf