Re: AMBER: Why I get the same TSTRA for different strucutures from Nmode calculation?

From: David A. Case <>
Date: Fri, 21 Nov 2003 15:33:38 -0800

On Fri, Nov 21, 2003, Yuqin Cai wrote:

> When I calculated the entropies using Nmode, I got exactly the same TSTRA
> (15.70 Kcal/mol)for all the 6 snapshots which were generated evenly from 5ns
> of dynamics simulation. Am I supposed to get a slightly difference between
> them just as the other terms like TSROT TSVIB? Any suggestions ?

Please send e-mail as plain text, not as html.

The translational entropy of a system does not depend in any way on its
conformation, so it must be expected that you would get the same results
for all snapshots.


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Fri Nov 21 2003 - 23:53:01 PST
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