[gmx-users] Gromacs force field discussion
patrick.fuchs at univ-paris-diderot.fr
Mon Mar 3 11:57:36 CET 2008
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.
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 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  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 aromatic groups from an unpublished paper from the Van Gusteren group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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