[gmx-users] Gromacs force field discussion
David van der Spoel
spoel at xray.bmc.uu.se
Mon Mar 3 12:01:44 CET 2008
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.
But the Berger et al force field is based upon OPLS, and hence it can be
combined with OPLS all atom FF.
> 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 aromatic groups from an unpublished paper from the Van Gusteren group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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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.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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