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

Berk Hess gmx3 at hotmail.com
Thu Dec 4 15:46:20 CET 2008 

Hi,

There are no good general purpose implicit solvent force fields.
But there are many around for specific purposes.
In Gromacs 4.1 there will be generalized Born implicit solvent,
but that will not be a lot faster than explicit water.

Berk

> Subject: RE: [gmx-users] Selecting force field for simulation in vacuum
> From: nazoia at det.uminho.pt
> To: gmx-users at gromacs.org
> Date: Thu, 4 Dec 2008 14:26:32 +0000
> 
> 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
> > > > 
> > > > _______________________________________________
> > > > gmx-users mailing list gmx-users at gromacs.org
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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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