[gmx-users] langevin dynamics

[Syma Khalid]

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)?

 

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

 

Many thanks in advance for your suggestions/comments,

 

-Syma

 

 

***********************************************************************
Dr Syma Khalid
RCUK Fellow (Chemical Biology)             
School of Chemistry
University of Southampton      
Highfield                              
Southampton      phone: (0)2380-594176
SO17 1BJ          email: S.Khalid at soton.ac.uk                          
U.K.
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