On Wed, Mar 10, 2004, rluo.uci.edu wrote:
>
> A question on temperature coupling option of ntt=1 when gb is used in
> sander of amber8. Is it normal that the average temperature is not equal
> to the target temperature as set by temp0 when the simulation system is
> very small, less than 300 atoms?
That is not normal, but in a 1000 step simulation, temp. fluctuations on
a 300 atom system can be quite noticeable, esp. if you are not
well-equilibrated.
I would strong recommend _against_ using ntt=1 for gb simulations; (this
is
also stated in the Amber manual). The Berendsen thermostat regulates the
total KE, but does nothing to ensure equipartition. It relies upon
collisions
to equalize the temperature at various points in the system, but with GB
there
are not so many collisions. In my view, ntt=3 is a much better option.
Try
gamma_ln somewhere around 5.
...good luck...dac
--
==================================================================
David A. Case | e-mail: case.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
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Received on Wed Apr 05 2006 - 23:50:04 PDT
