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

-- 

================================================================== David A. Case | e-mail: case_at_scripps.edu Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | http://www.scripps.edu/case ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu