[gmx-users] Re: Re:NVT equilibration of DMSO solvent (Charmm all-atom force field)

[Justin A. Lemkul]

udaya kiran marelli wrote:
> 
> Dear Mark Abraham,
> 
> Thank you for the reply.  However, I am sorry to tell you that I could 
> not find a tutorial that really is explicit to explain the procedure.  
> Could you please suggest some tutorial covering the non-water solvent 
> box generation and optimization using all-atom charmm force-field on 
> GROMACS.
> 

Please do not include the whole digest in your replies.  Cut and paste any 
relevant text and delete the rest.  Including the whole digest makes the archive 
terribly confusing.

To the point: there aren't going to be tutorials that cover every possible 
iteration of what someone wants to do.  Generate a reasonable starting 
configuration and equilibrate under an appropriate ensemble.  If you want 
explicit pointers on what may or may not be right or wrong with your .mdp 
settings, you need to post an .mdp file for comment.  Achieving a periodic 
system under NVT conditions is simple (and discussed in just about every 
tutorial, even if the goal of the tutorial is not explicitly what you want to 
do).  Set "pbc = xyz" and use the thermostat of your choice with no pressure 
coupling.  Presto - NVT ensemble.

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================