[gmx-users] Justin umbrella sampling tutorial......

Justin A. Lemkul jalemkul at vt.edu
Thu May 24 10:21:05 CEST 2012

On 5/24/12 8:19 AM, rama david wrote:
> Thank you for your reply,
> I am asking you again same question, EXTREMELY SORRY for my stupidity,
> In step six , I unable to differentiate npt and production run by
> mdp file as usualy we find difference by define term,
> I think I get meaning upto reason why to use -DPOSRES_B,
> but I want to know if we are using same mdp file in both condition
> means the npt equilibriation is as same as md production ,
> Then why to do npt, just run production md  with  DPOSRES_B

I'm not sure of what the question is exactly, so my apologies if the following 
explanation does not answer it.  For the tutorial, NPT is conducted with 
restraints on all protein heavy atoms.  The production runs are conducted by 
restraining only one chain for practical reasons.

Don't confuse yourself by always assuming that the difference between NPT and 
production runs is the use of define statements or position restraints.  There 
are many ways of doing equilibration.  NPT of a protein in solvent is typically 
done with restraints on the protein, allowing the solvent to relax and avoiding 
potential geometric distortions due to bad solvent contacts.  Production runs 
may or may not make use of any restraints.  Their use is dependent upon the 
situation at hand and whether or not they are appropriate.

I hope this explanation makes everything clear.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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