Volker Wirth wrote:
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.
As I read more about membrane simulation, I found this interesting article:
Shirley W. I. Siu, Robert Vácha, Pavel Jungwirth, and Rainer A. Böckmann
Biomolecular simulations of membranes: Physical properties from
different force fields
J. Chem. Phys. 128, 125103 (2008); DOI:10.1063/1.2897760
They compare GAFF, Berger and Charmm27 simulating a DOPC system with
experimental results. The best ff seems to be GAFF (Generalized Amber
FF, all atom), but there is no 'super' force field for _both_ membrane
and protein.
I am looking for a straightforward method to use in my diploma thesis
(time scale eight months). Combining different force fields
(Berger/GROMOS, Berger/OPLS) for lipids and proteins would be too
complex, also setting up GAFF for another lipid system (DMPC, DMPS and
mixed bilayers) won't be possible and in the moment the idea is to use
the paper's approach to get at least a simulation with **PC lipids.
I am curious to know what you believe to be "too complex" about the
GROMOS/Berger and OPLS/Berger combinations. Certainly arguments can be made
that combining force fields is questionable, but it's about the best we've got
for now. Using GROMOS with Berger effectively requires simple addition of
parameters to the correct locations in .itp files, and while using OPLS does
require a bit of work in making the correct conversions, it can be done in about
20 minutes if you use spreadsheet software.
Just something to consider. Good reference; I recently came across it as well.
-Justin
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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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