[gmx-users] Re: Where is the GROMOS87 force field when using pdb2gmx

Patrick Fuchs Patrick.Fuchs at ebgm.jussieu.fr
Thu Nov 8 19:10:12 CET 2007

Hi Erik,
but I did read many works in the literature that used G43a*, even yours 
in BJ (2006). I basically agree that the 'philosophy' of the Berger 
lipids is derived from OPLS, thus using this latter force field is 
probably best suited for peptide/lipid simulation in conjunction with 
Berger lipids (like in Tieleman et al 2006 J. Phys.: Condens. Matter 18 
S1221-S1234, or your last paper in press in Proteins). But apart from 
self-consistency, is it so a problem to mix Berger lipids with a GROMOS 
derived force field ? I ask you that because *many* previous works used 
Berger lipids with ffgmx (and this latter is probably still in use even 
if deprecated). So what is right ?
It would probably be worth doing a systematic comparison of the use of 
different protein force fields with Berger lipids. The above ref of P. 
Tieleman goes in this direction.


Erik Lindahl a écrit :
> Hi,
> On Nov 7, 2007, at 5:40 PM, maria goranovic wrote:
>> Thanks for the help, David. Actually, I just realized I was trying to
>> decide based on mailing list archives which, in some cases, are 5
>> years old. My mistake. I will use the 43a2 field for my protein.
>> Is there any standard procedure to combine 43a2 with the berger force
>> field (ffgmx) for lipids ?
> Don't do it. The berger force field is mostly derived from OPLS, so 
> you will (again) find it much easier to defend your choices if you mix 
> it with OPLS-AA/L instead.
> Cheers,
> Erik
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before 
> posting!
> Please don't post (un)subscribe requests to the list. Use thewww 
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

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
E-mail : Patrick.Fuchs at ebgm.jussieu.fr
Web Site: http://www.ebgm.jussieu.fr/~fuchs

More information about the gromacs.org_gmx-users mailing list