[gmx-users] how to run MD of a new molecule using OPLS
David van der Spoel
spoel at xray.bmc.uu.se
Wed Jan 9 08:07:11 CET 2008
Mark Abraham wrote:
> Egidijus Kuprusevicius wrote:
>> Could anyone tell me how to parameterize a new molecule for using it
>> with OPLS (basic principles).
> See http://wiki.gromacs.org/index.php/Parameterization
> > What a .pdb file should look like
> As normal, you need atom and residue names corresponding to those for
> your forcefield, as modified.
> > and what
> > .mdp variables are specificaly related to OPLS?
> None. That's not what .mdp parameters are for. Roughly speaking, the
> .top file and it's #includes define the model of physics for the system,
> and the .mdp file controls the choice of algorithms for the simulation.
> The two are interdependent, however.
To be more specific: some force field have been developed with a certain
cut-off treatment, and you might want to use the recommendations. On the
other hand you might want to evaluate the effects of these parameters
yourself. Both OPLS and GROMOS have been developed with certain cut-off
protocols, but many users now use them with PME.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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