Hi Mark,<br><br>The top md.log is below. The mdrun command was "mpirun -np 8 ~/software/bin/mdrun_mpi -deffnm md"<br><br><br> :-) G R O M A C S (-:<br><br> GROup of MAchos and Cynical Suckers<br>
<br> :-) VERSION 4.0.5 (-:<br><br><br> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br> Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br>
Copyright (c) 2001-2008, The GROMACS development team,<br> check out <a href="http://www.gromacs.org">http://www.gromacs.org</a> for more information.<br><br> This program is free software; you can redistribute it and/or<br>
modify it under the terms of the GNU General Public License<br> as published by the Free Software Foundation; either version 2<br> of the License, or (at your option) any later version.<br><br>
:-) /home/thamu/software/bin/mdrun_mpi (-:<br><br><br>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl<br>GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable<br>
molecular simulation<br>J. Chem. Theory Comput. 4 (2008) pp. 435-447<br>-------- -------- --- Thank You --- -------- --------<br><br><br>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.<br>
Berendsen<br>GROMACS: Fast, Flexible and Free<br>J. Comp. Chem. 26 (2005) pp. 1701-1719<br>-------- -------- --- Thank You --- -------- --------<br><br><br>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>E. Lindahl and B. Hess and D. van der Spoel<br>
GROMACS 3.0: A package for molecular simulation and trajectory analysis<br>J. Mol. Mod. 7 (2001) pp. 306-317<br>-------- -------- --- Thank You --- -------- --------<br><br><br>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>
H. J. C. Berendsen, D. van der Spoel and R. van Drunen<br>GROMACS: A message-passing parallel molecular dynamics implementation<br>Comp. Phys. Comm. 91 (1995) pp. 43-56<br>-------- -------- --- Thank You --- -------- --------<br>
<br>Input Parameters:<br> integrator = md<br> nsteps = 10000000<br> init_step = 0<br> ns_type = Grid<br> nstlist = 10<br> ndelta = 2<br>
nstcomm = 1<br> comm_mode = Linear<br> nstlog = 100<br> nstxout = 1000<br> nstvout = 0<br> nstfout = 0<br> nstenergy = 100<br>
nstxtcout = 0<br> init_t = 0<br> delta_t = 0.002<br> xtcprec = 1000<br> nkx = 70<br> nky = 70<br> nkz = 70<br>
pme_order = 4<br> ewald_rtol = 1e-05<br> ewald_geometry = 0<br> epsilon_surface = 0<br> optimize_fft = TRUE<br> ePBC = xyz<br> bPeriodicMols = FALSE<br>
bContinuation = FALSE<br> bShakeSOR = FALSE<br> etc = V-rescale<br> epc = Parrinello-Rahman<br> epctype = Isotropic<br> tau_p = 0.5<br>
ref_p (3x3):<br> ref_p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}<br> ref_p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}<br> ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}<br> compress (3x3):<br>
compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}<br> compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}<br> compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}<br> refcoord_scaling = No<br>
posres_com (3):<br> posres_com[0]= 0.00000e+00<br> posres_com[1]= 0.00000e+00<br> posres_com[2]= 0.00000e+00<br> posres_comB (3):<br> posres_comB[0]= 0.00000e+00<br> posres_comB[1]= 0.00000e+00<br>
posres_comB[2]= 0.00000e+00<br> andersen_seed = 815131<br> rlist = 1<br> rtpi = 0.05<br> coulombtype = PME<br> rcoulomb_switch = 0<br> rcoulomb = 1<br>
vdwtype = Cut-off<br> rvdw_switch = 0<br> rvdw = 1.4<br> epsilon_r = 1<br> epsilon_rf = 1<br> tabext = 1<br> implicit_solvent = No<br>
gb_algorithm = Still<br> gb_epsilon_solvent = 80<br> nstgbradii = 1<br> rgbradii = 2<br> gb_saltconc = 0<br> gb_obc_alpha = 1<br> gb_obc_beta = 0.8<br>
gb_obc_gamma = 4.85<br> sa_surface_tension = 2.092<br> DispCorr = No<br> free_energy = no<br> init_lambda = 0<br> sc_alpha = 0<br> sc_power = 0<br>
sc_sigma = 0.3<br> delta_lambda = 0<br> nwall = 0<br> wall_type = 9-3<br> wall_atomtype[0] = -1<br> wall_atomtype[1] = -1<br> wall_density[0] = 0<br>
wall_density[1] = 0<br> wall_ewald_zfac = 3<br> pull = no<br> disre = No<br> disre_weighting = Conservative<br> disre_mixed = FALSE<br> dr_fc = 1000<br>
dr_tau = 0<br> nstdisreout = 100<br> orires_fc = 0<br> orires_tau = 0<br> nstorireout = 100<br> dihre-fc = 1000<br> em_stepsize = 0.01<br>
em_tol = 10<br> niter = 20<br> fc_stepsize = 0<br> nstcgsteep = 1000<br> nbfgscorr = 10<br> ConstAlg = Lincs<br> shake_tol = 0.0001<br>
lincs_order = 4<br> lincs_warnangle = 30<br> lincs_iter = 1<br> bd_fric = 0<br> ld_seed = 1993<br> cos_accel = 0<br> deform (3x3):<br> deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> userint1 = 0<br> userint2 = 0<br> userint3 = 0<br>
userint4 = 0<br> userreal1 = 0<br> userreal2 = 0<br> userreal3 = 0<br> userreal4 = 0<br>grpopts:<br> nrdf: 6706.82 106800<br> ref_t: 300 300<br>
tau_t: 0.1 0.1<br>anneal: No No<br>ann_npoints: 0 0<br> acc: 0 0 0<br> nfreeze: N N N<br> energygrp_flags[ 0]: 0 0 0<br>
energygrp_flags[ 1]: 0 0 0<br> energygrp_flags[ 2]: 0 0 0<br> efield-x:<br> n = 0<br> efield-xt:<br> n = 0<br> efield-y:<br> n = 0<br> efield-yt:<br> n = 0<br> efield-z:<br> n = 0<br>
efield-zt:<br> n = 0<br> bQMMM = FALSE<br> QMconstraints = 0<br> QMMMscheme = 0<br> scalefactor = 1<br>qm_opts:<br> ngQM = 0<br>Table routines are used for coulomb: TRUE<br>
Table routines are used for vdw: FALSE<br>Will do PME sum in reciprocal space.<br><br>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen <br>
A smooth particle mesh Ewald method<br>J. Chem. Phys. 103 (1995) pp. 8577-8592<br>-------- -------- --- Thank You --- -------- --------<br><br>Using a Gaussian width (1/beta) of 0.320163 nm for Ewald<br>Cut-off's: NS: 1 Coulomb: 1 LJ: 1.4<br>
System total charge: -0.000<br>Generated table with 1200 data points for Ewald.<br>Tabscale = 500 points/nm<br>Generated table with 1200 data points for LJ6.<br>Tabscale = 500 points/nm<br>Generated table with 1200 data points for LJ12.<br>
Tabscale = 500 points/nm<br>Generated table with 1200 data points for 1-4 COUL.<br>Tabscale = 500 points/nm<br>Generated table with 1200 data points for 1-4 LJ6.<br>Tabscale = 500 points/nm<br>Generated table with 1200 data points for 1-4 LJ12.<br>
Tabscale = 500 points/nm<br><br>Enabling TIP4p water optimization for 17798 molecules.<br><br>Configuring nonbonded kernels...<br>Testing x86_64 SSE support... present.<br><br><br>Removing pbc first time<br><br>Initializing LINear Constraint Solver<br>
<br>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije<br>LINCS: A Linear Constraint Solver for molecular simulations<br>J. Comp. Chem. 18 (1997) pp. 1463-1472<br>
-------- -------- --- Thank You --- -------- --------<br><br>The number of constraints is 3439<br><br>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>S. Miyamoto and P. A. Kollman<br>SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid<br>
Water Models<br>J. Comp. Chem. 13 (1992) pp. 952-962<br>-------- -------- --- Thank You --- -------- --------<br><br>Center of mass motion removal mode is Linear<br>We have the following groups for center of mass motion removal:<br>
0: rest<br><br>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>G. Bussi, D. Donadio and M. Parrinello<br>Canonical sampling through velocity rescaling<br>J. Chem. Phys. 126 (2007) pp. 014101<br>-------- -------- --- Thank You --- -------- --------<br>
<br>There are: 56781 Atoms<br>There are: 17798 VSites<br>Max number of connections per atom is 59<br>Total number of connections is 216528<br>Max number of graph edges per atom is 4<br>Total number of graph edges is 113666<br>
<br>Constraining the starting coordinates (step 0)<br><br>Constraining the coordinates at t0-dt (step 0)<br>RMS relative constraint deviation after constraining: 3.77e-05<br>Initial temperature: 299.838 K<br><div class="gmail_quote">
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">> Recently I successfully installed the gromacs-4.0.5 mpi version.<br>
> I could run in 8 cpu. but the speed is very slow.<br>
> Total number of atoms in the system is 78424.<br>
> while running all 8 cpu showing 95-100% CPU.<br>
><br>
> How to speed up the calculation.<br>
><br>
> Thanks<br>
><br>
><br>
That's normal for a system that atoms/cpu ratio.<br>
What's your system and what mdp file are you using?<br>
--<br>
------------------------------------------------------<br>
You haven't given us any diagnostic information. The problem could be<br>
that you're not running an MPI GROMACS (show us your configure line,<br>
your mdrun command line and the top 50 lines of your .log file).<br>
<br>
Mark<br>
<br>
<br>
</blockquote></div><br>