[gmx-users] Selecting force field for simulation in vacuum
nazoia at det.uminho.pt
Thu Dec 4 12:42:12 CET 2008
I'm having some problems for selecting force field for a simulation in
vacuum. I'm using version 4.0.2.
According to pdb2gmx man page (pdb2gmx -h)
This program reads a pdb file, reads some database files, adds
the molecules and generates coordinates in Gromacs (Gromos)
format and a
topology in Gromacs format. These files can subsequently be
generate a run input file.
The force fields in the distribution are currently:
oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
G43b1 GROMOS96 43b1 Vacuum Forcefield
G43a1 GROMOS96 43a1 Forcefield
G43a2 GROMOS96 43a2 Forcefield (improved alkane dihedrals)
G45a3 GROMOS96 45a3 Forcefield
G53a5 GROMOS96 53a5 Forcefield
G53a6 GROMOS96 53a6 Forcefield
gmx Gromacs Forcefield (a modified GROMOS87, see manual)
encads Encad all-atom force field, using scaled-down vacuum
encadv Encad all-atom force field, using full solvent charges
Ok. I would like to use G43b1, but when I run
pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n system.ndx -i
posre.itp -inter -ignh
I just get this options, with no possibility for choosing G43b1:
Select the Force Field:
0: GROMOS96 43a1 force field
1: GROMOS96 43a2 force field (improved alkane dihedrals)
2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
6: [DEPRECATED] Gromacs force field (see manual)
7: [DEPRECATED] Gromacs force field with hydrogens for NMR
8: Encad all-atom force field, using scaled-down vacuum charges
9: Encad all-atom force field, using full solvent charges
I search on the mailing list for some solution and I get this message
from Berk Hess
The GROMOS96 G43b1 "vacuum" force field has been removed.
This confusing "vacuum" naming of this force field could make people
think that this force field was optimized for real vacuum simulations,
whereas it is actually G43a1 with neutralized charged residues.
This force field has never been used seriously.
Now I'm confused! Ok, there is no more G43b1.
So I would like to ask witch force field I can use for simulations in vaccum? If I search on the mailing list I get the advice of using G43b1.
Can anyone help me on this.
And just another small thing. Maybe it would be good to remove the reference to G43b1 on the pdb2gmx man page.
Thank you in advance.
Nuno Gonçalo Azoia Lopes
Laboratório de Investigação em Acabamento
Departamento de Engenharia Textil
Universidade do Minho
Campus de Azurém
Tel: +351 253 510 280 - Ext: 517 289
Fax: +351 253 510 293
Mobile: +351 965 382 487
E-mail: nazoia at det.uminho.pt
More information about the gromacs.org_gmx-users