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

Mark Abraham Mark.Abraham at anu.edu.au
Tue Nov 21 22:57:57 CET 2006

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
> “mdrun rerun” 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, “setting bonded and LJ parameter to zero” 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.


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