[gmx-users] Gromacs force field discussion
rainer at bioinformatik.uni-saarland.de
Mon Mar 3 14:10:36 CET 2008
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.
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
> 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.
> David van der Spoel a écrit :
>> Reay, Andrew wrote:
>>> 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
>> 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  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 plus changes on aromatic groups from an unpublished paper from the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.
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> !!!! new E-mail address: patrick.fuchs at univ-paris-diderot.fr !!!!
> 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
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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: rainer at bioinformatik.uni-saarland.de
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