[gmx-users] Gromacs force field discussion

[rainer]

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 plus changes on aromatic groups from an unpublished paper from the  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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>
> -- 
> _________________________________________________________________
> !!!! 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
http://www.bioinf.uni-sb.de/RB/
___________________________________________________________



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