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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 compounds.<br>For Gromos at least the liquid properties of alkanes have been 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 vacuum<br>> CC: <br>> <br>> GROMOS and OPLS were derived for condensed-phase properties, so none of those <br>> will be useful. I know nothing about ENCAD, however, but I do not 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 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 -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 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 people<br>> > think that this force field was optimized for real vacuum 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 in vaccum? If I search on the mailing list I get the advice of using G43b1.<br>> > Can anyone help me on this.<br>> > <br>> > And just another small thing. Maybe it would be good to remove the 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 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 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 /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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