[gmx-users] langevin dynamics

[Mark Abraham]

Syma Khalid wrote:
> Dear all,
> 
>  
> 
> I was wondering if someone could offer some advice?
> 
> I would like to run an atomistic langevin dynamics simulation (as I 
> don't want to include water explicitly). If I add the appropriate 
> langevin dynamics options in the mdp file, then is there any reason why 
> I shouldn't use explicit counter ions (unfortunately my protein has an 
> overall charge)?

In what medium are they going to move? How realistic is that going to be?

> Obviously I would use periodic boundary conditions so the ions don't 
> wander off.

If they really are just counter-ions, then simple electrostatics will do 
that... this is a side-issue, however.

Mark