[gmx-users] membrane with OPLS force field
Justin A. Lemkul
jalemkul at vt.edu
Wed Aug 6 21:29:49 CEST 2008
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.
> - 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
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>> Justin A. Lemkul
>> Graduate Research Assistant
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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