Lucio Montero wrote:
Hello!
What is the best force field to use for a MD of a compley of three
proteins and an organic molecule. And what are the best temperature and
pressure coupling methods.
"Best" is completely subjective, based on what you read about different force
fields and which one you think will be the most accurate for your system.
Another consideration is that organic molecule, and how reasonable it will be to
develop parameters for it (based on the derivation of the force field you
choose). Beware that parameterization is a very advanced topic, and should not
be attempted by a newcomer to MD.
As far as temperature and pressure coupling (as well as the force field
selection), there is no substitute for reading the primary literature for the
common methods - Berendsen, Nose-Hoover, etc. and choosing wisely. Read about
the different methods in the Gromacs manual, and you will be able to find the
citations for these methods.
-Justin
Best regards.
Lucio.
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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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