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

Thu Dec 4 15:26:32 CET 2008

Hi,

Well, what I really need is a simulations without the solvent, because
solvent calculations are time consuming, especially for water.

What do you mean by "implicit solvent"? I check the mailing list and I
have found some discussions about this, and I've found some papers that
now I need to read.

Please, correct me if I'm wrong. Implicit solvent would be a system with
no solvent molecules, being all calculations made as if there were
solvent. Can I just do a "normal" simulations, with the same parameters
I've use before, but without solvent molecules in the .gro (or any
other) file? I've found some references to implicit_solvent option
in .mdp file but I can't find it on the manual. Is it necessary?

As I understand, you use PME for such calculations. In the mailing list
I found a reference for an article that I would like to read but I can't
downloaded (Phys. Rev. Lett. 96, 147801 (2006)).

Ok, now it's up to me. I'm thankful for all the help. I have some good
reading ahead of me.

Nuno Azoia

On Thu, 2008-12-04 at 13:36 +0100, Berk Hess wrote:
> Hi,
> 
> It depends on what you mean with vacuum simulation.
> Do you mean really simulating how a protein would behave in vacuum?
> Or do you want some type of implicit solvent?
> 
> OPLS has been parametrized on the properties of pure liquids of small
> compounds.
> For Gromos at least the liquid properties of alkanes have been
> checked.
> So both force fields would work well for real vacuum simulations.
> 
> Berk
> 
> 
> > Date: Thu, 4 Dec 2008 07:17:12 -0500
> > From: jalemkul at vt.edu
> > To: nazoia at det.uminho.pt; gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Selecting force field for simulation in
> vacuum
> > CC: 
> > 
> > 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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