Re: amber-developers: MD with GB

From: David A. Case <>
Date: Wed, 10 Mar 2004 14:49:43 -0700

On Wed, Mar 10, 2004, 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

I would strong recommend _against_ using ntt=1 for gb simulations; (this
also stated in the Amber manual). The Berendsen thermostat regulates the
total KE, but does nothing to ensure equipartition. It relies upon
to equalize the temperature at various points in the system, but with GB
are not so many collisions. In my view, ntt=3 is a much better option.
gamma_ln somewhere around 5.

...good luck...dac

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 Wed Apr 05 2006 - 23:50:04 PDT
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