[gmx-users] ElecStatic for two residues and mdrun rerun issues
Mark.Abraham at anu.edu.au
Tue Nov 21 22:57:57 CET 2006
> 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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