[gmx-users] membrane with OPLS force field
chris.neale at utoronto.ca
Tue Aug 5 16:11:50 CEST 2008
Sorry for my misunderstanding.
You can not use standard OPLS parameters for lipids. Even if you go through the paramaterization process
(see the gromace wiki and the original OPLS papers) then you are still stuck with the fact that
standard acyl chain parameters fail when they get too long. I think there ref. for that is a Berendsen paper
on hexadecane simulations, but I could be wrong there. In any event, 'protein' parameters do not appear to
transfer directly to long acyl chains in a simple way and therefore your non-coulombic parameters may also
need to be parameterized.
I understand your motivation to do this, and of course your parameters would be widely accepted if they produced
good bulk properties, but we're talking about an entire phd project here, so I suggest that you don't plan to
have this up and running from scratch in the next few months.
-- original message --
Ok, thank you very much. However, with this combination I am not using all atoms for the lipds,
if I am right and my intention was using all atoms both for the protein and the membrane.
Thank you very much for your help.
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