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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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