<br>Dear gmx users,<br><br>I am trying to run grompp program to preprocess the input files. input<br>
> gro file contains coordinates of a stack of hexane molecules (256<br>
> molecules)..<br><br>1- In the outpout file I see two notes. As with note 1, Could you please help me understand what wrong with charge group is. <br><br>2- Also, my system includes hydrocarbons (hexane as solvent and later I will add polyethylene). I am interested in vdw forces. I need your help regarding note 2 which is saying sth on electrostatic forces and coloumb cut -off. Which setting is the best for my system.<br>
<br>3- in mdp file, what is the sauitable setting for cpp.<br><br><br>
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<pre class="western">grompp -f em -c Hexane-stack-<span lang="en-US">Residuename </span>.gro -p HexaneModified-<span lang="en-US">Residuename</span>.top -o Hexane_em >& output.grompp_em</pre>
<br>Many many thanks for your help. :)<br><br><br>***************************************output file:<br><br>ption Filename Type Description<br>------------------------------------------------------------<br>
-f em.mdp Input, Opt! grompp input file with MD parameters<br> -po mdout.mdp Output grompp input file with MD parameters<br> -c Hexane-stack-Residuename.gro Input Structure file: gro g96 pdb<br>
tpr tpb 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 HexaneModified-Residuename.top Input Topology file<br> -pp processed.top Output, Opt. Topology file<br> -o Hexane_em.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<br><br><b>Ignoring obsolete mdp entry 'cpp</b>'<br>checking input for internal consistency...<br>Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp<br>
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp<br>Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp<br>Generated 332520 of the 332520 non-bonded parameter combinations<br>
Generating 1-4 interactions: fudge = 0.5<br>Generated 332520 of the 332520 1-4 parameter combinations<br>Excluding 3 bonded neighbours molecule type 'HEX'<br>processing coordinates...<br>double-checking input for internal consistency...<br>
renumbering atomtypes...<br>converting bonded parameters...<br><br><b>NOTE 1 [file HexaneModified-Residuename.top, line unknown]:<br> The largest charge group contains 20 atoms.<br> Since atoms only see each other when the centers of geometry of the charge</b><br>
Option Filename Type Description<br>------------------------------------------------------------<br> -f em.mdp Input, Opt! grompp input file with MD parameters<br>ption Filename Type Description<br>
------------------------------------------------------------<br> -f em.mdp Input, Opt! grompp input file with MD parameters<br> -po mdout.mdp Output grompp input file with MD parameters<br><br><br>-c Hexane-stack-Residuename.gro Input Structure file: gro g96 pdb<br>
tpr tpb 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 HexaneModified-Residuename.top Input Topology file<br> -pp processed.top Output, Opt. Topology file<br> -o Hexane_em.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<br><br>Option Type Value Description<br> groups they belong to are within the cut-off distance, too large charge<br> groups can lead to serious cut-off artifacts.<br>
For efficiency and accuracy, charge group should consist of a few atoms.<br> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.<br><br>initialising group options...<br>processing index file...<br>Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat<br>
Making dummy/rest group for T-Coupling containing 5120 elements<br>Making dummy/rest group for Acceleration containing 5120 elements<br>Making dummy/rest group for Freeze containing 5120 elements<br>Making dummy/rest group for Energy Mon. containing 5120 elements<br>
Making dummy/rest group for VCM containing 5120 elements<br>Number of degrees of freedom in T-Coupling group rest is 15357.00<br><br>Making dummy/rest group for User1 containing 5120 elements<br>Making dummy/rest group for User2 containing 5120 elements<br>
Making dummy/rest group for XTC containing 5120 elements<br>Making dummy/rest group for Or. Res. Fit containing 5120 elements<br>Making dummy/rest group for QMMM containing 5120 elements<br>T-Coupling has 1 element(s): rest<br>
Energy Mon. has 1 element(s): rest<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): rest<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><br><b>NOTE 2 [file em.mdp, line unknown]:<br>
You are using a plain Coulomb cut-off, which might produce artifacts.<br> You might want to consider using PME electrostatics.</b><br><br><br>writing run input file...<br><br>There were 2 notes<br>gcq#39: "Yeah, a Wuzz, Or a Jerk" (F. Black)<br>
<br> :-) G R O M A C S (-:<br><br> S C A M O R G<br><br> :-) VERSION 4.0.7 (-:<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> :-) grompp (double precision) (-:<br><br>processing topology...<br>Analysing residue names:<br>There are: 256 OTHER residues<br>
There are: 0 PROTEIN residues<br>There are: 0 DNA residues<br><br>*****************************************************<br>em.mdp file I use:<br>
><br>
> ;title = cpeptide<br>
> cpp = /lib/cpp<br>
> define = -DFLEX_SPC<br>
> constraints = none<br>
> integrator = steep<br>
> dt = 0.002 ; ps !<br>
> nsteps = 100<br>
> nstlist = 10<br>
> ns_type = grid<br>
> rlist = 1.0<br>
> rcoulomb = 1.0<br>
> rvdw = 1.0<br>
> ;<br>
> ; Energy minimizing stuff<br>
> ;<br>
> emtol = 1000.0<br>
> emstep = 0.01<br>
><br>*************************************************************<br><br>