Re: [AMBER] thermal averaging of properties

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Wed, 18 Nov 2020 19:54:34 +0530

Dear David,
thanks a lot for confirming the same.
best regards

On Wed, Nov 18, 2020 at 7:49 PM David A Case <david.case.rutgers.edu> wrote:

> On Wed, Nov 18, 2020, Vaibhav Dixit wrote:
>
> >I have a requirement to estimate thermal averages of Amber-FF Es.
> >For this, I have calculated SP energies for all snapshots, and Amber-FF Es
> >are printed in the mdout files.
> >Now my assumption is that a simple average (as printed by the "statistics"
> >option of mdout_analyzer.py) isn't the thermal average of the Es that I
> >want here.
>
> It sound's like a simple average is what you want. Snapshots from an MD
> simulation sample a Boltzmann distribution for the force field you are
> using. So, the simple average of a mechanical quantity like energy is
> indeed
> a "thermal average".
>
> ....dac
>
>
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-- 
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
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Received on Wed Nov 18 2020 - 06:30:05 PST
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