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

[Patrick Fuchs]

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.
Cheers,

Patrick

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
>
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-- 
_______________________________________________________
Patrick FUCHS
Equipe de Bioinformatique Genomique et Moleculaire
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