[gmx-users] Problem about *FF

[Justin A. Lemkul]

Quoting sudheer babu <sudheer.pbm07 at gmail.com>:

>  Thank you very much Mr.Andreas for reply,
> As I told you, used deprecated FF for protein, after insertion into POPC
> bilayer, ran 4ns production. is it compulsory to use opls/gromos43a6 *ff for
> run simulation protein in water? I have repeat to the whole process because
> wrong usage of depracated *FF. Pls help me....
> Thanks for your invaluable help........
>

I believe it is most advisable to avoid the ffgmx force field.  There was a
recent discussion on this topic as a matter of fact, so have a look through the
list archive from the past few weeks.  There is also a paper out from Tieleman's
group (2006? 2007?) that recommends using OPLS in conjunction with the Berger
lipid parameters to get the best results.  You would then have to conduct your
simulations in water under OPLS as well to get results that can be compared.

-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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