[AMBER] Re-Imaging Trajectories

From: Parker de Waal <Parker.deWaal09.kzoo.edu>
Date: Tue, 9 Jul 2013 22:07:51 -0400

Hi AMBER Users!

I've seen a number of tutorials on the amber website reference re-imaging
trajectories, however I was wondering if someone could explain the
significance of this action to me.

>From my knowledge it seems that re-imaging a trajectory, after a simulation
has been run, removes excess waters that have moved out of the original box
coordinates. In terms of NVE simulations would it be advantageous to run a
short 1-2 ns simulation, re-image the trajectory, and then use the new
trajectory coordinates to continue with a full 20 ns NVE simulation?

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Received on Tue Jul 09 2013 - 19:30:02 PDT
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