Dear Mark, Thanks for your untiring efforts to reply back to all. Regards, B.Nataraj On Wed, 22 Nov 2006 16:41:40 +1100, "Mark Abraham" <[EMAIL PROTECTED]> said: > 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. :-) > > 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 - Access all of your messages and folders wherever you are _______________________________________________ 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
