[gmx-users] Re: Where is the GROMOS87 force field when using pdb2gmx
Patrick.Fuchs at ebgm.jussieu.fr
Thu Nov 8 19:10:12 CET 2007
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 :
> 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.
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