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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--
========================================
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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