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<div>Hi</div>
<div>I am using Gromacs version 4.0.5.</div>
<div>I put one protein in a simulation box with water molecules and CL- only.</div>
<div>My simulation broke at the step, Relaxation of solvent and hydrogen atom position.</div>
<div>Here are the .top file, command, output of the grommp, pr.mdp.</div>
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<div>anything wrong here?</div>
<div>Thank you</div>
<div>Lin</div>
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<div><strong><font size="4">[6YZ.top]</font></strong></div>
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<div>[ molecules ]<br>; Compound #mols<br>Protein_A 1<br>SOL 6504<br>CL- 8<br> <br></div>
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<div><span lang="EN-US" style="FONT-SIZE: 12pt; COLOR: red; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-fareast-language: AR-SA; mso-ansi-language: EN-US; mso-bidi-language: AR-SA"><strong>Relaxation of solvent and hydrogen atom positions: Position restrained MD</strong></span></div>
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<div><strong><font size="4">[command]</font></strong></div>
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<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Times New Roman" size="3">grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr </font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Times New Roman" size="3"> </font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Times New Roman" size="3">mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-PR </font></span></p></div>
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<div><strong><font size="4">[output of the grompp comand]</font></strong></div>
<div>grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr<br> :-) G R O M A C S (-:</div>
<div> Gyas ROwers Mature At Cryogenic Speed</div>
<div> :-) VERSION 4.0.5 (-:</div>
<div><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.</div>
<div> 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.</div>
<div> :-) grompp_mpi (-:</div>
<div>Option Filename Type Description<br>------------------------------------------------------------<br> -f pr.mdp Input, Opt! grompp input file with MD parameters<br> -po mdout.mdp Output grompp input file with MD parameters<br>
-c 6LYZ-EM-solvated.gro Input Structure file: gro g96 pdb tpr tpb<br> tpa<br> -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br> -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br>
-n index.ndx Input, Opt. Index file<br> -p 6LYZ.top Input Topology file<br> -pp processed.top Output, Opt. Topology file<br> -o 6LYZ-PR.tpr Output Run input file: tpr tpb tpa<br> -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt<br>
-e ener.edr Input, Opt. Energy file: edr ene</div>
<div>Option Type Value Description<br>------------------------------------------------------<br>-[no]h bool no Print help info and quit<br>-nice int 0 Set the nicelevel<br>-[no]v bool yes Be loud and noisy<br>
-time real -1 Take frame at or first after this time.<br>-[no]rmvsbds bool yes Remove constant bonded interactions with virtual<br> sites<br>-maxwarn int 0 Number of allowed warnings during input processing<br>
-[no]zero bool no Set parameters for bonded interactions without<br> defaults to zero instead of generating an error<br>-[no]renum bool yes Renumber atomtypes and minimize number of<br>
atomtypes</div>
<div>Ignoring obsolete mdp entry 'cpp'<br>Replacing old mdp entry 'unconstrained-start' by 'continuation'</div>
<div>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#<br>checking input for internal consistency...</div>
<div>NOTE 1 [file pr.mdp, line unknown]:<br> The Berendsen thermostat does not generate the correct kinetic energy<br> distribution. You might want to consider using the V-rescale thermostat.</div>
<div>processing topology...<br>Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG45a3.itp<br>Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG45a3nb.itp<br>Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG45a3bon.itp<br>
Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ff_dum.itp<br>Generated 141 of the 1176 non-bonded parameter combinations<br>Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ions.itp<br>Excluding 3 bonded neighbours molecule type 'Protein_A'<br>
turning all bonds into constraints...<br>Excluding 2 bonded neighbours molecule type 'SOL'<br>turning all bonds into constraints...<br>Excluding 1 bonded neighbours molecule type 'CL-'<br>turning all bonds into constraints...<br>
processing coordinates...<br>double-checking input for internal consistency...<br>Velocities were taken from a Maxwell distribution at 200 K<br>Reading position restraint coords from 6LYZ-EM-solvated.gro<br>renumbering atomtypes...<br>
converting bonded parameters...<br>initialising group options...<br>processing index file...<br>Analysing residue names:<br>Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/aminoacids.dat<br>There are: 6512 OTHER residues<br>
There are: 129 PROTEIN residues<br>There are: 0 DNA residues<br>Analysing Protein...<br>Analysing Other...<br>Making dummy/rest group for Acceleration containing 20841 elements<br>Making dummy/rest group for Freeze containing 20841 elements<br>
Making dummy/rest group for VCM containing 20841 elements<br>Number of degrees of freedom in T-Coupling group Protein is 2618.00<br>Number of degrees of freedom in T-Coupling group Non-Protein is 39048.00<br>Making dummy/rest group for User1 containing 20841 elements<br>
Making dummy/rest group for User2 containing 20841 elements<br>Making dummy/rest group for Or. Res. Fit containing 20841 elements<br>Making dummy/rest group for QMMM containing 20841 elements<br>T-Coupling has 2 element(s): Protein Non-Protein<br>
Energy Mon. has 2 element(s): Protein Non-Protein<br>Acceleration has 1 element(s): rest<br>Freeze has 1 element(s): rest<br>User1 has 1 element(s): rest<br>User2 has 1 element(s): rest<br>
VCM has 1 element(s): rest<br>XTC has 1 element(s): System<br>Or. Res. Fit has 1 element(s): rest<br>QMMM has 1 element(s): rest<br>Checking consistency between energy and charge groups...<br>
This run will generate roughly 3 Mb of data<br>writing run input file...</div>
<div>There was 1 note</div>
<div>Back Off! I just backed up 6LYZ-PR.tpr to ./#6LYZ-PR.tpr.1#</div>
<div>gcq#264: "RTFM" (B. Hess)<br></div>
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<div><strong><font size="4">[pr.mdp]</font></strong></div>
<div><strong><font size="4"></font></strong> </div>
<div>; VARIOUS PREPROCESSING OPTIONS<br>title = <br>cpp = /lib/cpp<br>include = <br>define = -DPOSRES</div>
<div>; RUN CONTROL PARAMETERS<br>integrator = md<br>tinit = 0<br>dt = 0.001<br>nsteps = 5000<br>nstcomm = 0</div>
<div>; OUTPUT CONTROL OPTIONS<br>nstxout = 0<br>nstvout = 0<br>nstfout = 0<br>nstlog = 10<br>nstenergy = 1<br>nstxtcout = 0<br>
xtc_precision = 1000<br>xtc-grps = System<br>energygrps = Protein Non-Protein</div>
<div>; NEIGHBORSEARCHING PARAMETERS<br>nstlist = 5<br>ns-type = Grid<br>pbc = xyz<br>rlist = 0.9</div>
<div>; OPTIONS FOR ELECTROSTATICS AND VDW<br>coulombtype = Reaction-Field<br>rcoulomb = 1.4<br>epsilon_rf = 78<br>epsilon_r = 1<br>vdw-type = Cut-off<br>
rvdw = 1.4</div>
<div>; Temperature coupling <br>Tcoupl = Berendsen<br>tc-grps = Protein Non-Protein<br>tau_t = 0.1 0.1<br>ref_t = 200 200</div>
<div>; Pressure coupling <br>Pcoupl = No</div>
<div>; GENERATE VELOCITIES FOR STARTUP RUN<br>gen_vel = yes<br>gen_temp = 200.0<br>gen_seed = 1735</div>
<div>; OPTIONS FOR BONDS <br>constraints = all-bonds<br>constraint-algorithm = Lincs<br>unconstrained-start = no<br>lincs-order = 4<br>lincs-iter = 1<br>lincs-warnangle = 30</div>
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