AMBER Archive (2003)

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

From: David A. Case (case_at_scripps.edu)
Date: Fri Nov 21 2003 - 17:33:38 CST

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.

..dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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