Re: [gmx-users] Gromacs force field discussion
Hi David, since updated GROMOS force fields are now available within GROMACS, I agree one does not need to use ffgmx, at least for standard simulations. The only problem is for lipid/protein simulations. The only publicly available I know that runs under GROMACS is the combination of Berger lipids with ffgmx (on the website of Peter Tieleman). For someone starting a project of lipid/protein simulations, there is a priori no other public alternative (using GROMACS), although I know some new parameters are about to be published. Cheers, Patrick David van der Spoel a écrit : Reay, Andrew wrote: Hi, 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. 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GROMOS87 + changes due to Van Buuren Berendsen (J.Phys.Chem. 97 [1993] 9206) plus changes on aromatic groups from an unpublished paper from the Van Gusteren group (these parameters are given in my paper in J.Biomol.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. Andy ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- _ new E-mail address: [EMAIL PROTECTED] Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 Web Site: http://www.ebgm.jussieu.fr/~fuchs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs force field discussion
patrick fuchs wrote: Hi David, since updated GROMOS force fields are now available within GROMACS, I agree one does not need to use ffgmx, at least for standard simulations. The only problem is for lipid/protein simulations. The only publicly available I know that runs under GROMACS is the combination of Berger lipids with ffgmx (on the website of Peter Tieleman). For someone starting a project of lipid/protein simulations, there is a priori no other public alternative (using GROMACS), although I know some new parameters are about to be published. Cheers, But the Berger et al force field is based upon OPLS, and hence it can be combined with OPLS all atom FF. Patrick David van der Spoel a écrit : Reay, Andrew wrote: Hi, 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. 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. Andy ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs force field discussion
David van der Spoel wrote: patrick fuchs wrote: Hi David, since updated GROMOS force fields are now available within GROMACS, I agree one does not need to use ffgmx, at least for standard simulations. The only problem is for lipid/protein simulations. The only publicly available I know that runs under GROMACS is the combination of Berger lipids with ffgmx (on the website of Peter Tieleman). For someone starting a project of lipid/protein simulations, there is a priori no other public alternative (using GROMACS), although I know some new parameters are about to be published. Cheers, But the Berger et al force field is based upon OPLS, and hence it can be combined with OPLS all atom FF. These parameters were developed with united-atom OPLS. Tieleman and co-workers introduced modifications to allow the usage of these parameters with all atom OPLS (Tieleman et al., J. Phys. Condens. Matter 18 S1221-34, 2006). I would use it with cautious though, the results show significant differences between ffgmx and OPLSAA (Table 1 of the paper above). In addition, there can be an error in the range of 10 kCal/mol in the calculated cyclohexane to water transfer energies with OPLS (in any combination, Table 3 of Tieleman et al.). I found this alarming, but haven't seen results from other FFs - the error may be just as big. Ran. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs force field discussion
Hi Patrick, 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. Best, Rainer On Mar 3, 2008, at 11:57 AM, patrick fuchs wrote: Hi David, since updated GROMOS force fields are now available within GROMACS, I agree one does not need to use ffgmx, at least for standard simulations. The only problem is for lipid/protein simulations. The only publicly available I know that runs under GROMACS is the combination of Berger lipids with ffgmx (on the website of Peter Tieleman). For someone starting a project of lipid/protein simulations, there is a priori no other public alternative (using GROMACS), although I know some new parameters are about to be published. Cheers, Patrick David van der Spoel a écrit : Reay, Andrew wrote: Hi, 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. 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. Andy ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- _ new E-mail address: [EMAIL PROTECTED] Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 Web Site: http://www.ebgm.jussieu.fr/~fuchs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php __ Dr. Rainer Böckmann Theoretical Computational Membrane Biology Center for Bioinformatics Saar Universität des Saarlandes Gebäude C7.1, EG D-66041 Saarbrücken, Germany Phone: ++49 +681 302-64169 / 68627 FAX: ++49 +681 302-64180 E-Mail: [EMAIL PROTECTED] http://www.bioinf.uni-sb.de/RB/ ___ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Gromacs force field discussion
Hi, 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. Andy ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
