Volker Wirth wrote:
Hi Justin,
thanks a lot for your response! Of course my mail was a bit
"provocative", as I know that combination methods are state of the
art, used in many publications and leading to reasonable results.
(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
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
What I had in mind was that combining different force fields (which
represent different models of nature) increases the complexity of the
simulation and we need to do more intensive tests on the results, to
prove that we don't actually observe an effect of "interference" or
something like that.
There is this paper by Tieleman et al.:
Membrane protein simulations with a united-atom lipid and all-atom
protein model: lipid–protein interactions, side chain transfer free
energies and model proteins
D Peter Tieleman et al 2006 J. Phys.: Condens. Matter 18 S1221-S1234
doi: 10.1088/0953-8984/18/28/S07
They point out that finding parameters for combined systems is a very
delicate problem (it is possible, though) - so the idea to use one
force field for the complete system looks much more inviting for me
(and the paper of Shirley et al. presents very good results for their
system with GAFF - _without_ protein, of course).
OK, I'm not yet sure about the method I should use...
Definitely a quandary I know many of us face. There isn't one perfect,
self-consistent force field. Maybe one day :) Each has its limitations, and so
far the combination method seems to be the most widely used. Up to you to do
whatever you feel is the most justifiable.
-Justin
- Volker
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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========================================
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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