Re: AMBER: Energy fluctuations

From: David A. Case <>
Date: Tue, 8 Mar 2005 11:36:14 -0800

On Tue, Mar 08, 2005, wrote:
> I would like to monitor energy fluctuations at every timestep of
> my protein simlation, however energy fluctuations are only included in the
> final output. I am curious if anyone else has extracted this data from their
> simulation results, and if so what is the procedure that was used? If no one
> has done this before, can anyone suggest a method for coding such an analysis
> program?

By setting the ntave parameter in sander, you can get fluctuation reports
at whatever frequency you request. If this is not what you need, my guess
that you will have to set ntwe to 1, and then process the mden file with
your own script to get the statistics you need.

.....good luck...dac

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Received on Tue Mar 08 2005 - 19:53:02 PST
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