[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:
>> Hi,
>> 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.

> Mark
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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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