Log file opened on Thu Mar 12 15:53:42 2009 Host: e4hpc01 pid: 23358 nodeid: 0 nnodes: 8 The Gromacs distribution was built Thu Mar 12 14:40:48 CET 2009 by root@e4hpc01 (Linux 2.6.18-53.el5 x86_64) :-) G R O M A C S (-: Gnomes, ROck Monsters And Chili Sauce :-) 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. :-) /root/NFS/Gromacs/bin/mdrun_mpi_d (double precision) (-: ++++ 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 --- -------- -------- parameters of the run: integrator = md nsteps = 50000 init_step = 0 ns_type = Grid nstlist = 10 ndelta = 2 nstcomm = 1 comm_mode = Linear nstlog = 10 nstxout = 250 nstvout = 1000 nstfout = 0 nstenergy = 10 nstxtcout = 0 init_t = 0 delta_t = 0.002 xtcprec = 1000 nkx = 64 nky = 64 nkz = 63 pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 0 epsilon_surface = 0 optimize_fft = TRUE ePBC = xyz bPeriodicMols = FALSE bContinuation = FALSE bShakeSOR = FALSE etc = Berendsen epc = Parrinello-Rahman epctype = Isotropic tau_p = 0.5 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]={ 4.50000e-05, 0.00000e+00, 0.00000e+00} compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00} compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-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 = 1.4 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: 3489.83 56703.2 41.9979 ref_t: 300 300 300 tau_t: 0.1 0.1 0.1 anneal: No No No ann_npoints: 0 0 0 acc: 0 0 0 nfreeze: 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 Initializing Domain Decomposition on 8 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.614 nm, LJ-14, atoms 1485 1492 multi-body bonded interactions: 0.614 nm, Proper Dih., atoms 1485 1492 Minimum cell size due to bonded interactions: 0.675 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.876 nm Estimated maximum distance required for P-LINCS: 0.876 nm This distance will limit the DD cell size, you can override this with -rcon Using 0 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 8 cells with a minimum initial size of 1.095 nm The maximum allowed number of cells is: X 5 Y 5 Z 5 Domain decomposition grid 4 x 2 x 1, separate PME nodes 0 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. 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: 1.4 System total charge: 0.000 Generated table with 4799 data points for Ewald. Tabscale = 2000 points/nm Generated table with 4799 data points for LJ6. Tabscale = 2000 points/nm Generated table with 4799 data points for LJ12. Tabscale = 2000 points/nm Generated table with 4799 data points for 1-4 COUL. Tabscale = 2000 points/nm Generated table with 4799 data points for 1-4 LJ6. Tabscale = 2000 points/nm Generated table with 4799 data points for 1-4 LJ12. Tabscale = 2000 points/nm Enabling SPC water optimization for 9451 molecules. Configuring nonbonded kernels... Testing x86_64 SSE2 support... present. Removing pbc first time Initializing Parallel LINear Constraint Solver ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess P-LINCS: A Parallel Linear Constraint Solver for molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 116-122 -------- -------- --- Thank You --- -------- -------- The number of constraints is 1787 There are inter charge-group constraints, will communicate selected coordinates each lincs iteration ++++ 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 6229 inter charge-group exclusions, will use an extra communication step for exclusion forces for PME The initial number of communication pulses is: X 1 Y 1 The initial domain decomposition cell size is: X 1.55 nm Y 3.02 nm The maximum allowed distance for charge groups involved in interactions is: non-bonded interactions 1.400 nm (the following are initial values, they could change due to box deformation) two-body bonded interactions (-rdd) 1.400 nm multi-body bonded interactions (-rdd) 1.400 nm atoms separated by up to 5 constraints (-rcon) 1.551 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 2 Y 1 The minimum size for domain decomposition cells is 1.082 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.70 Y 0.46 The maximum allowed distance for charge groups involved in interactions is: non-bonded interactions 1.400 nm two-body bonded interactions (-rdd) 1.400 nm multi-body bonded interactions (-rdd) 1.082 nm atoms separated by up to 5 constraints (-rcon) 1.082 nm Making 2D domain decomposition grid 4 x 2 x 1, home cell index 0 0 0 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: 30126 Atoms Charge group distribution at step 0: 1295 1280 1281 1276 1309 1258 1283 1274 Grid: 11 x 13 x 9 cells Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (step 0) RMS relative constraint deviation after constraining: 3.73e-05 Initial temperature: 300.99 K