[gmx-users] ElecStatic for two residues and mdrun rerun issues

raja raja_28 at fastmail.us
Wed Nov 22 08:10:00 CET 2006

Dear Mark,
Thanks for your untiring efforts to reply back to all.

On Wed, 22 Nov 2006 16:41:40 +1100, "Mark Abraham"
<Mark.Abraham at anu.edu.au> said:
> raja wrote:
> > Thanks Mark for your reply. So the &#8220;parameters nstlist=0&#8221;,
> > &#8220;unconstrained_start=yes&#8221;,  using &#8220;energygrp_excl&#8221;  will help to speed
> > up the " mdrun rerun" ? , That is what I can understand after reading
> > about those parameters picked up by you from manual. Before your mail
> > reached, I ran rerun without any of those parameters changed in original
> > mdp file but removed &#8220;Protein, SOL, NA etc.,&#8221; from &#8220;energygrp&#8221; instead I
> > put two groups representing two amino acid residues,whose potentials to
> > be computed. It took half an hour for &#8220;mdrun &#8211;rurun&#8221;  for trajectory of
> > 2ns length.
> > 
> > So I will satisfied by my this run, if you can confirm me the
> > introduction or alteration of those parameters is meant for only speedup
> > purpose and not for anything else....
> This is where you should be using your judgement, not mine. Why didn't 
> doing the aforementioned reading, after the searching manual for 
> "rerun", answer your questions? I don't know anything about this issue 
> except what I've read there...
> If you have a specific question about a fact or interpretation, then go 
> right ahead and ask, but unless you're paying for a support and 
> consultancy contract, nobody's going to go out of their way to do any 
> work for you. :-)
> Mark
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