On 6/29/12 9:04 AM, massimo sandal wrote:
On 29 Jun 2012 14:08, "Justin A. Lemkul" <jalem...@vt.edu
<mailto:jalem...@vt.edu>>
>
> The settings in my tutorial are for use with OPLS-AA and are thus not
suitable for a simulation with CHARMM. Cutoffs and other aspects will be
different.
This is interesting. In general, where can you find optimal mdp settings for
each force field?
By reading the primary literature for how each force field was derived. The
parameters are only guaranteed to work within the context of correct cutoffs,
electrostatic schemes, neighborlist update interval, water model used, etc.
Some older force fields have been demonstrated to work well with PME even if
originally derived with RF or some other method, but generally the other
settings must adhere to the original parameterization. Some force fields can be
very sensitive to these incorrect settings.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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