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
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