AMBER Archive (2007)

Subject: AMBER: RE: A little question

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Jul 26 2007 - 09:51:55 CDT

Dear Guowei,
 
The units in the energy plots are indeed KCal/Mol they are simply extracted
from the AMBER output file without and modification or scaling - thus the
results should be the same as if you "grepped" out the total energy etc.
 
I'm not sure what you mean by a random value of total energy. The magnitude
of the value is not of great use in and of itself since the origin is kind
of arbitrary - For most MD simulations the origin does not actually lie
within the accessible phase space. What is important is the difference
between energies of various conformations - this should have the essentially
the same magnitude as a pure QM calculation would yield. If however, by your
question you mean the energy fluctuations are too large to be KCal/Mol then
you will need to explain things some more. Particularly why you conclude
that the fluctuations are too large.
 
All the best
Ross

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From: gwyin [mailto:gwyin_at_chem.ruc.edu.cn]
Sent: Thursday, July 26, 2007 05:10
To: Ross Walker
Subject: A little question

 
Dear Dr. Ross,
  I have a simple question to ask you. In the tutorial of Amber you have
setted a ".perl" script to extract the detailed information from the MD
result file".out". I wonder what the energy unit in the energy vs time plot?
Someone believe it's "Kcal/mol", but for a random value of total energy in
the file is too large to think it's kcal/mol?
 
Appreciate you!
With best
 
Guowei-Yin
Department of Chemistry, RUC

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