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Hi,<br><br>There are no good general purpose implicit solvent force fields.<br>But there are many around for specific purposes.<br>In Gromacs 4.1 there will be generalized Born implicit solvent,<br>but that will not be a lot faster than explicit water.<br><br>Berk<br><br>> Subject: RE: [gmx-users] Selecting force field for simulation in vacuum<br>> From: nazoia@det.uminho.pt<br>> To: gmx-users@gromacs.org<br>> Date: Thu, 4 Dec 2008 14:26:32 +0000<br>> <br>> Hi,<br>> <br>> Well, what I really need is a simulations without the solvent, because<br>> solvent calculations are time consuming, especially for water.<br>> <br>> What do you mean by "implicit solvent"? I check the mailing list and I<br>> have found some discussions about this, and I've found some papers that<br>> now I need to read.<br>> <br>> Please, correct me if I'm wrong. Implicit solvent would be a system with<br>> no solvent molecules, being all calculations made as if there were<br>> solvent. Can I just do a "normal" simulations, with the same parameters<br>> I've use before, but without solvent molecules in the .gro (or any<br>> other) file? I've found some references to implicit_solvent option<br>> in .mdp file but I can't find it on the manual. Is it necessary?<br>> <br>> As I understand, you use PME for such calculations. In the mailing list<br>> I found a reference for an article that I would like to read but I can't<br>> downloaded (Phys. Rev. Lett. 96, 147801 (2006)).<br>> <br>> Ok, now it's up to me. I'm thankful for all the help. I have some good<br>> reading ahead of me.<br>> <br>> Nuno Azoia<br>> <br>> <br>> On Thu, 2008-12-04 at 13:36 +0100, Berk Hess wrote:<br>> > Hi,<br>> > <br>> > It depends on what you mean with vacuum simulation.<br>> > Do you mean really simulating how a protein would behave in vacuum?<br>> > Or do you want some type of implicit solvent?<br>> > <br>> > OPLS has been parametrized on the properties of pure liquids of small<br>> > compounds.<br>> > For Gromos at least the liquid properties of alkanes have been<br>> > checked.<br>> > So both force fields would work well for real vacuum simulations.<br>> > <br>> > Berk<br>> > <br>> > <br>> > > Date: Thu, 4 Dec 2008 07:17:12 -0500<br>> > > From: jalemkul@vt.edu<br>> > > To: nazoia@det.uminho.pt; gmx-users@gromacs.org<br>> > > Subject: Re: [gmx-users] Selecting force field for simulation in<br>> > vacuum<br>> > > CC: <br>> > > <br>> > > GROMOS and OPLS were derived for condensed-phase properties, so none<br>> > of those <br>> > > will be useful. I know nothing about ENCAD, however, but I do not<br>> > often see it <br>> > > in the literature.<br>> > > <br>> > > -Justin<br>> > > <br>> > > Nuno Azoia wrote:<br>> > > > Hello everyone!<br>> > > > <br>> > > > I'm having some problems for selecting force field for a<br>> > simulation in<br>> > > > vacuum. I'm using version 4.0.2.<br>> > > > According to pdb2gmx man page (pdb2gmx -h)<br>> > > > <br>> > > > DESCRIPTION<br>> > > > -----------<br>> > > > This program reads a pdb file, reads some database files, adds<br>> > > > hydrogens to<br>> > > > the molecules and generates coordinates in Gromacs (Gromos)<br>> > > > format and a<br>> > > > topology in Gromacs format. These files can subsequently be<br>> > > > processed to<br>> > > > generate a run input file. <br>> > > > <br>> > > > The force fields in the distribution are currently:<br>> > > > <br>> > > > oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)<br>> > > > G43b1 GROMOS96 43b1 Vacuum Forcefield <br>> > > > G43a1 GROMOS96 43a1 Forcefield <br>> > > > G43a2 GROMOS96 43a2 Forcefield (improved alkane dihedrals)<br>> > > > G45a3 GROMOS96 45a3 Forcefield <br>> > > > G53a5 GROMOS96 53a5 Forcefield <br>> > > > G53a6 GROMOS96 53a6 Forcefield <br>> > > > gmx Gromacs Forcefield (a modified GROMOS87, see manual)<br>> > > > encads Encad all-atom force field, using scaled-down vacuum<br>> > > > charges<br>> > > > encadv Encad all-atom force field, using full solvent charges<br>> > > > <br>> > > > <br>> > > > Ok. I would like to use G43b1, but when I run<br>> > > > <br>> > > > pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n system.ndx<br>> > -i<br>> > > > posre.itp -inter -ignh<br>> > > > <br>> > > > I just get this options, with no possibility for choosing G43b1:<br>> > > > <br>> > > > Select the Force Field:<br>> > > > 0: GROMOS96 43a1 force field <br>> > > > 1: GROMOS96 43a2 force field (improved alkane dihedrals)<br>> > > > 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)<br>> > > > 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) <br>> > > > 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) <br>> > > > 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)<br>> > > > 6: [DEPRECATED] Gromacs force field (see manual)<br>> > > > 7: [DEPRECATED] Gromacs force field with hydrogens for NMR<br>> > > > 8: Encad all-atom force field, using scaled-down vacuum charges<br>> > > > 9: Encad all-atom force field, using full solvent charges <br>> > > > <br>> > > > <br>> > > > I search on the mailing list for some solution and I get this<br>> > message<br>> > > > from Berk Hess<br>> > > > (http://www.gromacs.org/component/option,com_wrapper/Itemid,165/)<br>> > > > <br>> > > > The GROMOS96 G43b1 "vacuum" force field has been removed.<br>> > > > This confusing "vacuum" naming of this force field could make<br>> > people<br>> > > > think that this force field was optimized for real vacuum<br>> > simulations,<br>> > > > whereas it is actually G43a1 with neutralized charged residues.<br>> > > > This force field has never been used seriously.<br>> > > > <br>> > > > Now I'm confused! Ok, there is no more G43b1.<br>> > > > So I would like to ask witch force field I can use for simulations<br>> > in vaccum? If I search on the mailing list I get the advice of using<br>> > G43b1.<br>> > > > Can anyone help me on this.<br>> > > > <br>> > > > And just another small thing. Maybe it would be good to remove the<br>> > reference to G43b1 on the pdb2gmx man page.<br>> > > > <br>> > > > Thank you in advance.<br>> > > > <br>> > > > Nuno Azoia<br>> > > > <br>> > > > --<br>> > > > <br>> > > > Nuno Gonçalo Azoia Lopes<br>> > > > <br>> > > > Laboratório de Investigação em Acabamento<br>> > > > Departamento de Engenharia Textil<br>> > > > Universidade do Minho<br>> > > > Campus de Azurém<br>> > > > 4800-058 Guimarães<br>> > > > Portugal<br>> > > > <br>> > > > Tel: +351 253 510 280 - Ext: 517 289<br>> > > > Fax: +351 253 510 293<br>> > > > <br>> > > > Mobile: +351 965 382 487<br>> > > > E-mail: nazoia@det.uminho.pt<br>> > > > <br>> > > > _______________________________________________<br>> > > > gmx-users mailing list gmx-users@gromacs.org<br>> > > > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > > > Please search the archive at http://www.gromacs.org/search before<br>> > posting!<br>> > > > Please don't post (un)subscribe requests to the list. Use the <br>> > > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > > > <br>> > > <br>> > > -- <br>> > > ========================================<br>> > > <br>> > > Justin A. Lemkul<br>> > > Graduate Research Assistant<br>> > > Department of Biochemistry<br>> > > Virginia Tech<br>> > > Blacksburg, VA<br>> > > jalemkul[at]vt.edu | (540) 231-9080<br>> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> > > <br>> > > ========================================<br>> > > _______________________________________________<br>> > > gmx-users mailing list gmx-users@gromacs.org<br>> > > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > > Please search the archive at http://www.gromacs.org/search before<br>> > posting!<br>> > > Please don't post (un)subscribe requests to the list. Use the <br>> > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > <br>> > <br>> > ______________________________________________________________________<br>> > <br>> > Express yourself instantly with MSN Messenger! MSN Messenger <br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the <br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. 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