[gmx-users] Understanding of OPLS-all atomic FF

[Justin A. Lemkul]

Are you referring to the POPC structure available from Tieleman's site, 
and thus the parameters found in lipid.itp and popc.itp?  Those are 
united-atom structures.  The parameters for them were based in part on 
OPLS parameters, hence the argument can be made that the OPLS-AA force 
field can be used in conjunction with these parameters, if one is 
careful to keep the force fields consistent (i.e., Chris Neale's procedure).

-Justin

minnale wrote:
>
>  
> Hi all,
> this may be a trivial question to you that, I am using OPLS-all 
> atomic  FF for both protein and lipids. When I do protein simulations 
> I can say that simulating protein with OPLS-all atomic FF by noticing 
> protein.gro contain all atoms(N,H,C-alpha,HA1,HA2,C,O for Glycine 
> etc...) for each amino acid residue, but I have doubt that how can you 
> say that popc type lipids are simulating with OPLS-all atomic FF? if I 
> open popc.gro files,couldnt able to find difference between atom types 
> of opls-FF or gromos96 43a1 or some other FF.
>
> Thanks in advance. 
>
>
>
> Amity
>
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-- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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