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.... B.Nataraj On Wed, 22 Nov 2006 08:57:57 +1100, "Mark Abraham" <[EMAIL PROTECTED]> 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 > > “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. > > Mark > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Faster than the air-speed velocity of an unladen european swallow _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
