Log file opened on Fri Mar 23 12:07:20 2012 Host: tcbpc170 pid: 4388 nodeid: 0 nnodes: 1 The Gromacs distribution was built Fri Feb 24 15:27:34 CET 2012 by sabine@tcbpc170 (Linux 2.6.30.10-105.2.23.fc11.x86_64 x86_64) :-) G R O M A C S (-: Giving Russians Opium May Alter Current Situation :-) VERSION 4.5.5 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, 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) 2001-2010, 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 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 = steep nsteps = 100 init_step = 0 ns_type = Grid nstlist = 1 ndelta = 2 nstcomm = 10 comm_mode = Linear nstlog = 100 nstxout = 100 nstvout = 100 nstfout = 0 nstcalcenergy = -1 nstenergy = 100 nstxtcout = 0 init_t = 0 delta_t = 0.001 xtcprec = 1000 nkx = 45 nky = 45 nkz = 90 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 = No 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 andersen_seed = 815131 rlist = 1.2 rlistlong = 1.2 rtpi = 0.05 coulombtype = PME rcoulomb_switch = 0 rcoulomb = 1.2 vdwtype = Cut-off rvdw_switch = 0 rvdw = 1.2 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 free_energy = yes init_lambda = 0.05 delta_lambda = 0 n_foreign_lambda = 0 sc_alpha = 0.7 sc_power = 1 sc_sigma = 0.3 sc_sigma_min = 0.3 nstdhdl = 10 separate_dhdl_file = yes dhdl_derivatives = yes dh_hist_size = 0 dh_hist_spacing = 0.1 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 = Simple 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 = 1000 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: 50427 ref_t: 0 tau_t: 0 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 Initializing Domain Decomposition on 2 nodes Dynamic load balancing: no Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 3.341 nm, LJC Pairs NB, atoms 22476 22761 multi-body bonded interactions: 0.649 nm, Angle, atoms 1668 1686 Minimum cell size due to bonded interactions: 3.675 nm Using 0 separate PME nodes Optimizing the DD grid for 2 cells with a minimum initial size of 3.675 nm The maximum allowed number of cells is: X 1 Y 1 Z 2 Domain decomposition grid 1 x 1 x 2, separate PME nodes 0 PME domain decomposition: 2 x 1 x 1 Domain decomposition nodeid 0, coordinates 0 0 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. 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 0.384195 nm for Ewald Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2 System total charge, top. A: -0.000 top. B: 5.000 Generated table with 1100 data points for Ewald. Tabscale = 500 points/nm Generated table with 1100 data points for LJ6. Tabscale = 500 points/nm Generated table with 1100 data points for LJ12. Tabscale = 500 points/nm Generated table with 1100 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1100 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1100 data points for 1-4 LJ12. Tabscale = 500 points/nm Enabling SPC-like water optimization for 5953 molecules. Configuring nonbonded kernels... Configuring standard C nonbonded kernels... Testing x86_64 SSE2 support... present. There are 304 atoms and 304 charges for free energy perturbation 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 --- -------- -------- Linking all bonded interactions to atoms There are 55376 inter charge-group exclusions, will use an extra communication step for exclusion forces for PME The initial number of communication pulses is: Z 1 The initial domain decomposition cell size is: Z 5.09 nm The maximum allowed distance for charge groups involved in interactions is: non-bonded interactions 1.200 nm two-body bonded interactions (-rdd) 4.213 nm multi-body bonded interactions (-rdd) 4.213 nm