<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi Patrick,</div><div><br class="webkit-block-placeholder"></div><div>we recently parametrized DOPC in the generalized Amber FF (GAFF). The Gromacs input files (itp & top, mdp) as well as a pdb file are available on our website. </div><div><br class="webkit-block-placeholder"></div><div>Best,</div><div>Rainer</div><br><div><div>On Mar 3, 2008, at 11:57 AM, patrick fuchs wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi David,<br>since updated GROMOS force fields are now available within GROMACS, I<br>agree one does not need to use ffgmx, at least for standard simulations.<br>The only problem is for lipid/protein simulations. The only publicly<br>available I know that runs under GROMACS is the combination of Berger<br>lipids with ffgmx (on the website of Peter Tieleman). For someone<br>starting a project of lipid/protein simulations, there is a priori no<br>other public alternative (using GROMACS), although I know some new<br>parameters are about to be published.<br>Cheers,<br><br>Patrick<br><br>David van der Spoel a écrit :<br><blockquote type="cite">Reay, Andrew wrote:<br></blockquote><blockquote type="cite"><blockquote type="cite">Hi,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I am trying to find out why the Gromacs force field is no longer recommended for use. I've searched the mailing list archives for quite awhile to find the discussion but have been unsuccessful. Can anybody tell me where to find that discussion? Thanks very much.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite">The never has bee a GROMACS force field, although we named it such to avoid confusion with official "GROMOS" force fields. What used to be called the GROMACS force field was basically GROMOS87 + changes due to Van Buuren & Berendsen (J.Phys.Chem. 97 [1993] 9206) plus changes on aromatic groups from an unpublished paper from the Van Gusteren group (these parameters are given in my paper in J.Biomol. NMR 8 (1996) p.229). This is described in the manual. In other words there is no good description of ths force field in a single paper. For good reasons the Van Gunsteren group have updated their GROMOS force field on a number of occasions, and these force field are now supported in GROMACS, along with a few others. Although it is still possible to use the old parameter set, please do not call it "The GROMACS force field", but use the description above. Most referees fro scientific papers will (should) raise their eyebrows when reading that this parameter set was used, so this is another reason to shy away from it.<br></blockquote><blockquote type="cite"><blockquote type="cite">Andy<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">_______________________________________________<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></blockquote><br>-- <br>_________________________________________________________________<br>!!!! new E-mail address: <a href="mailto:patrick.fuchs@univ-paris-diderot.fr">patrick.fuchs@univ-paris-diderot.fr</a> !!!!<br>Patrick FUCHS<br>Equipe de Bioinformatique Genomique et Moleculaire<br>INSERM U726, Universite Paris 7<br>Case Courrier 7113<br>2, place Jussieu, 75251 Paris Cedex 05, FRANCE<br>Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30<br>Web Site: <a href="http://www.ebgm.jussieu.fr/~fuchs">http://www.ebgm.jussieu.fr/~fuchs</a><br><br><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><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 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></blockquote></div><br><div> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>__________________________________________________________<br>Dr. Rainer Böckmann<br>Theoretical & Computational Membrane Biology<br>Center for Bioinformatics Saar<br>Universität des Saarlandes<br>Gebäude C7.1, EG<br>D-66041 Saarbrücken, Germany<br>Phone: ++49 +681 302-64169 / 68627 FAX: ++49 +681 302-64180<br>E-Mail: <a href="mailto:rainer@bioinformatik.uni-saarland.de">rainer@bioinformatik.uni-saarland.de</a><br><a href="http://www.bioinf.uni-sb.de/RB/">http://www.bioinf.uni-sb.de/RB/</a><br>___________________________________________________________<br></div><div><br></div></div></div></span><br class="Apple-interchange-newline"> </div><br></body></html>