[gmx-users] Hydrocarbon system, help on mdp setting +output file
Moeed
lecielll at googlemail.com
Sat Apr 24 04:03:23 CEST 2010
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.
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.
3- in mdp file, what is the sauitable setting for cpp.
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
>
*************************************************************
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