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

Mark Abraham Mark.Abraham at anu.edu.au
Wed Nov 22 06:41:40 CET 2006

raja wrote:
> Thanks Mark for your reply. So the “parameters nstlist=0”,
> “unconstrained_start=yes”,  using “energygrp_excl”  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 “Protein, SOL, NA etc.,” from “energygrp” instead I
> put two groups representing two amino acid residues,whose potentials to
> be computed. It took half an hour for “mdrun –rurun”  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. :-)


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