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

raja raja_28 at fastmail.us
Wed Nov 22 06:26:18 CET 2006

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....



On Wed, 22 Nov 2006 08:57:57 +1100, "Mark Abraham"
<Mark.Abraham at anu.edu.au> said:
> raja wrote:
> > Hi gmxions,
> > 
> > I am interested in calculating electrostatic potential between chosen
> > residues (Two amino acid) versus function of simulation time. To do that
> > I have created two groups for two residues in index file and want to do
> > &#8220;mdrun rerun&#8221; further. This is where I struggle; I am looking for some
> > help to understand what is the mandatory adjustment in parameters to be
> > effected before doing "mdrun rerun". 
> I don't think there are any "mandatory adjustments", except, as the 
> manual notes, you probably want nstlist=0, unconstrained_start=yes and 
> to use energygrp_excl. I found this through the highly difficult process 
> of searching the GROMACS manual for the word "rerun". Perhaps you should 
> do this too.
> > I saw some replies regarding this
> > issue by saying, &#8220;setting bonded and LJ parameter to zero&#8221; and more.
> This sounds like garbage, or something someone else was doing in their 
> particular rerun. This quote would be more useful to everyone if you 
> provided a link to the page you found it on.
> Mark
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  raja_28 at fastmail.us

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