[gmx-users] Gromacs force field discussion

patrick fuchs patrick.fuchs at univ-paris-diderot.fr
Mon Mar 3 11:57:36 CET 2008

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.


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 aromatic groups from an unpublished paper from the Van Gusteren group 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
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