RE: AMBER: Suggestion regarding long simulation.

From: Yong Duan <>
Date: Thu, 18 Sep 2003 20:33:30 -0400

You probably do not have to save the trajectories often. Otherwise, get
ready for a decent size hard drive.
Leave plenty of room for molecule to expand. At 30-ns time scale,
depending on the stability and simulation condition, main-chain RMSD in
the loop region can be as large as 5-6A or even beyond. You probably do
not like the scenario where you have to redo the simulation because you
(or your boss) found part of the molecule touches another part of the
same molecule through PBC image at 29ns.
Good luck!
By the way, you can write your script in a way to check and resubmit
your job automatically and automate the whole thing. You then can go on
vacation for a month or so and your boss won't even notice your absence.
Welcome any
suggestion regarding this.

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Received on Fri Sep 19 2003 - 01:53:02 PDT
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