[gmx-users] Force field selection

Justin A. Lemkul jalemkul at vt.edu
Thu Dec 4 19:31:47 CET 2008

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.


> 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


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