[gmx-users] how to run MD of a new molecule using OPLS

[Mark Abraham]

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.

Mark