[gmx-users] Hydrocarbon system, help on mdp setting +output file
Justin A. Lemkul
jalemkul at vt.edu
Sat Apr 24 04:10:17 CEST 2010
Moeed wrote:
>
> Dear gmx users,
>
> I am trying to run grompp program to preprocess the input files. input
> > gro file contains coordinates of a stack of hexane molecules (256
> > molecules)..
>
> 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.
>
Please see the manual, section 4.6.2. If a charge group is too large, its
center of mass may be beyond the cutoff, so no interactions will be calculated,
when, in fact, atoms within the group are actually be interacting. So, with a
large charge group, you will almost certainly miss electrostatic interactions.
The note from grompp actually tells you pretty much exactly how to build
appropriate charge groups. You can't get much better than that :)
> 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.
>
For energy minimization, it's probably not a major factor. Plain cutoffs give
nasty truncation artefacts and were only really useful decades ago when
computers were far slower. Again, read the manual about the methods that are
implemented in Gromacs and any literature about their benefits and limitations.
> 3- in mdp file, what is the sauitable setting for cpp.
>
The cpp parameter is irrelevant in Gromacs 4.0.x, since grompp has its own cpp.
-Justin
>
> grompp -f em -c Hexane-stack-Residuename .gro -p HexaneModified-Residuename.top -o Hexane_em >& output.grompp_em
>
>
> Many many thanks for your help. :)
>
>
> ***************************************output file:
>
> ption Filename Type Description
> ------------------------------------------------------------
> -f em.mdp Input, Opt! grompp input file with MD parameters
> -po mdout.mdp Output grompp input file with MD parameters
> -c Hexane-stack-Residuename.gro Input Structure file: gro g96 pdb
> tpr tpb tpa
> -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
> -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
> -n index.ndx Input, Opt. Index file
> -p HexaneModified-Residuename.top Input Topology file
> -pp processed.top Output, Opt. Topology file
> -o Hexane_em.tpr Output Run input file: tpr tpb tpa
> -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
> -e ener.edr Input, Opt. Energy file: edr ene
>
> *Ignoring obsolete mdp entry 'cpp*'
> checking input for internal consistency...
> Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp
> Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp
> Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp
> Generated 332520 of the 332520 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 332520 of the 332520 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'HEX'
> processing coordinates...
> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
>
> *NOTE 1 [file HexaneModified-Residuename.top, line unknown]:
> The largest charge group contains 20 atoms.
> Since atoms only see each other when the centers of geometry of the
> charge*
> Option Filename Type Description
> ------------------------------------------------------------
> -f em.mdp Input, Opt! grompp input file with MD parameters
> ption Filename Type Description
> ------------------------------------------------------------
> -f em.mdp Input, Opt! grompp input file with MD parameters
> -po mdout.mdp Output grompp input file with MD parameters
>
>
> -c Hexane-stack-Residuename.gro Input Structure file: gro g96 pdb
> tpr tpb tpa
> -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
> -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
> -n index.ndx Input, Opt. Index file
> -p HexaneModified-Residuename.top Input Topology file
> -pp processed.top Output, Opt. Topology file
> -o Hexane_em.tpr Output Run input file: tpr tpb tpa
> -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
> -e ener.edr Input, Opt. Energy file: edr ene
>
> Option Type Value Description
> groups they belong to are within the cut-off distance, too large charge
> groups can lead to serious cut-off artifacts.
> For efficiency and accuracy, charge group should consist of a few atoms.
> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
>
> initialising group options...
> processing index file...
> Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat
> Making dummy/rest group for T-Coupling containing 5120 elements
> Making dummy/rest group for Acceleration containing 5120 elements
> Making dummy/rest group for Freeze containing 5120 elements
> Making dummy/rest group for Energy Mon. containing 5120 elements
> Making dummy/rest group for VCM containing 5120 elements
> Number of degrees of freedom in T-Coupling group rest is 15357.00
>
> Making dummy/rest group for User1 containing 5120 elements
> Making dummy/rest group for User2 containing 5120 elements
> Making dummy/rest group for XTC containing 5120 elements
> Making dummy/rest group for Or. Res. Fit containing 5120 elements
> Making dummy/rest group for QMMM containing 5120 elements
> T-Coupling has 1 element(s): rest
> Energy Mon. has 1 element(s): rest
> Acceleration has 1 element(s): rest
> Freeze has 1 element(s): rest
> User1 has 1 element(s): rest
> User2 has 1 element(s): rest
> VCM has 1 element(s): rest
> XTC has 1 element(s): rest
> Or. Res. Fit has 1 element(s): rest
> QMMM has 1 element(s): rest
> Checking consistency between energy and charge groups...
>
> *NOTE 2 [file em.mdp, line unknown]:
> You are using a plain Coulomb cut-off, which might produce artifacts.
> You might want to consider using PME electrostatics.*
>
>
> writing run input file...
>
> There were 2 notes
> gcq#39: "Yeah, a Wuzz, Or a Jerk" (F. Black)
>
> :-) G R O M A C S (-:
>
> S C A M O R G
>
> :-) VERSION 4.0.7 (-:
>
>
> 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.
>
> :-) grompp (double precision) (-:
>
> processing topology...
> Analysing residue names:
> There are: 256 OTHER residues
> There are: 0 PROTEIN residues
> There are: 0 DNA residues
>
> *****************************************************
> em.mdp file I use:
> >
> > ;title = cpeptide
> > cpp = /lib/cpp
> > define = -DFLEX_SPC
> > constraints = none
> > integrator = steep
> > dt = 0.002 ; ps !
> > nsteps = 100
> > nstlist = 10
> > ns_type = grid
> > rlist = 1.0
> > rcoulomb = 1.0
> > rvdw = 1.0
> > ;
> > ; Energy minimizing stuff
> > ;
> > emtol = 1000.0
> > emstep = 0.01
> >
> *************************************************************
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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