AMBER Archive (2008)

Subject: AMBER: Energy calculation and replica exchange in Amber9

From: Li Dawei (lidawei_at_gmail.com)
Date: Thu Mar 13 2008 - 08:50:49 CDT

Hi, Forks:

I found out that the potential energy sander provided in file mden at
step N was actually the energy of step N-1's coordinated set.

That is, if you print coordinates and energy both at 1000 step
interval, the coordinates set will be 1000's, 2000's, .... but the
energy will be 999's, 1999'....., etc.

This is generally not a problem in MD simulation. However, this may
cause the Replica Exchange MD to use the wrong energy (one step
backward) when calculating exchange possibility. I wonder whether this
will make the result of RE MD unpredictable? Does anyone have any idea
about this?

thanks.

dawei
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