[gmx-users] Selecting force field for simulation in vacuum

[Justin A. Lemkul]

GROMOS and OPLS were derived for condensed-phase properties, so none of those 
will be useful.  I know nothing about ENCAD, however, but I do not often see it 
in the literature.

-Justin

Nuno Azoia wrote:
> Hello everyone!
> 
> 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)
> 
>         DESCRIPTION
>         -----------
>         This program reads a pdb file, reads some database files, adds
>         hydrogens to
>         the molecules and generates coordinates in Gromacs (Gromos)
>         format and a
>         topology in Gromacs format. These files can subsequently be
>         processed to
>         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
>         charges
>         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
> (http://www.gromacs.org/component/option,com_wrapper/Itemid,165/)
> 
>         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 Azoia
> 
> --
> 
> Nuno Gonçalo Azoia Lopes
> 
> Laboratório de Investigação em Acabamento
> Departamento de Engenharia Textil
> Universidade do Minho
> Campus de Azurém
> 4800-058 Guimarães
> Portugal
> 
> 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
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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