[AMBER] thermal averaging of properties

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Wed, 18 Nov 2020 11:58:11 +0900

Dear All,
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.
The histogram option shows that the Es have an almost Boltzmann
distribution (attached figure).
Thus do I need to scale the Es by some factor before taking an average so
that it becomes the thermal average? If yes, is it possible to derive this
factor from the normalization coefficient that appears on the y-axis of the
histogram? The mdout_analyzer doesn't allow to print the histogram freq,
bins or normalization factors in a text file.

Thus in short, can you please help me understand how to derive the thermal
averages of energies for MD trajectories.
I realize that my understanding of the physical-chemistry concepts related
to these topics might be weak, thus valuable insights and corrections in
this approach (if necessary) are highly appreciated.

Thank you and best regards.

Dr. Vaibhav A. Dixit,
Assistant Professor,
Department of Pharmacy,
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
ORCID ID: https://orcid.org/0000-0003-4015-2941
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Received on Tue Nov 17 2020 - 23:00:03 PST
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