Log file opened on Tue Mar 17 01:56:48 2009 Host: bingo pid: 12001 nodeid: 0 nnodes: 1 The Gromacs distribution was built Thu Dec 11 17:19:34 IST 2008 by manik@bingo (Linux 2.6.24-22-generic i686) :-) G R O M A C S (-: GROtesk MACabre and Sinister :-) 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 = 1000000 init_step = 0 ns_type = Grid nstlist = 10 ndelta = 2 nstcomm = 0 comm_mode = None nstlog = 0 nstxout = 125 nstvout = 125 nstfout = 0 nstenergy = 125 nstxtcout = 250000 init_t = 0 delta_t = 0.001 xtcprec = 1000 nkx = 0 nky = 0 nkz = 0 pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 0 epsilon_surface = 0 optimize_fft = FALSE ePBC = xy bPeriodicMols = FALSE bContinuation = FALSE bShakeSOR = FALSE etc = Berendsen 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 = 2.7 rtpi = 0.05 coulombtype = Shift rcoulomb_switch = 0 rcoulomb = 2.5 vdwtype = Shift rvdw_switch = 0 rvdw = 2.5 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 = constraint pull_geometry = direction pull_dim (3): pull_dim[0]=1 pull_dim[1]=1 pull_dim[2]=1 pull_r1 = 1 pull_r0 = 1.5 pull_constr_tol = 1e-06 pull_nstxout = 10 pull_nstfout = 1 pull_ngrp = 1 pull_group 0: atom (672): atom[0,...,671] = {672,...,1343} weight: not available pbcatom = 1007 vec (3): vec[0]= 0.00000e+00 vec[1]= 0.00000e+00 vec[2]= 0.00000e+00 init (3): init[0]= 0.00000e+00 init[1]= 0.00000e+00 init[2]= 0.00000e+00 rate = 0 k = 0 kB = 0 pull_group 1: atom (672): atom[0,...,671] = {0,...,671} weight: not available pbcatom = 335 vec (3): vec[0]= 1.00000e+00 vec[1]= 0.00000e+00 vec[2]= 0.00000e+00 init (3): init[0]= 2.08088e+00 init[1]= 0.00000e+00 init[2]= 0.00000e+00 rate = 1 k = 0 kB = 0 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: 5975 ref_t: 300 tau_t: 0.1 anneal: No ann_npoints: 0 acc: 0 0 0 0 0 0 nfreeze: Y Y Y N N N energygrp_flags[ 0]: 0 0 energygrp_flags[ 1]: 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: TRUE Using shifted Lennard-Jones, switch between 0 and 2.5 nm Cut-off's: NS: 2.7 Coulomb: 2.5 LJ: 2.5 System total charge: 0.000 Generated table with 1850 data points for Shift. Tabscale = 500 points/nm Generated table with 1850 data points for LJ6Shift. Tabscale = 500 points/nm Generated table with 1850 data points for LJ12Shift. Tabscale = 500 points/nm Configuring nonbonded kernels... Testing AMD 3DNow support... not present. Testing ia32 SSE support... present. Removing pbc first time Will apply constraint COM pulling in geometry 'direction' between a reference group and 1 group Pull group 0: 672 atoms, mass 672.000 Pull group 1: 672 atoms, mass 672.000 ++++ 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: 2664 Atoms Max number of connections per atom is 0 Total number of connections is 0 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: 310.324 K Started mdrun on node 0 Tue Mar 17 01:56:48 2009 Step Time Lambda 0 0.00000 0.00000 Grid: 18 x 18 x 1 cells Energies (kJ/mol) LJ (SR) Coulomb (SR) Potential Kinetic En. Total Energy -6.56439e+00 0.00000e+00 -6.56439e+00 7.62164e+03 7.61508e+03 Temperature Pressure (bar) 3.06834e+02 0.00000e+00