Dear Amber developers and users,
I use sander to (re)calculate energy and force
from an obtained MD trajectory by setting "imin = 5".
There, I found that a MD trajectory which was preliminarily RMSd-fit on a
coordinates
shows "blow-up" of energy and force.
I guess that due to usage of PME...but it still remains unclear for me.
I am grateful if you give an answer for this question
and let me know how to avoid it after RMS-fit for MD trajectory, if possible.
Yours sincerely,
Ikuo KURISAKI
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Received on Wed May 22 2013 - 05:30:03 PDT
