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plus changes on aromatic groups from an unpublished paper from the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
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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: [EMAIL PROTECTED]
http://www.bioinf.uni-sb.de/RB/
___________________________________________________________
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