AMBER Archive (2006)

Subject: Re: AMBER: temperature regulation

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Tue Jul 18 2006 - 06:41:18 CDT

actually the manual suggests using ntt=3, which is Langevin dynamics.
Langevin has options, as does Andersen, and the appropriate
choices really depend on what problem you are trying to solve
and what data you want to get out of the simulation.
I would suggest reading articles that were successful in the
type of research that you want to do and follow their example.

Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) wrote:

>Dear all,
>
>I am using the sander module of amber 9. I found in the manual that the weack
>coupling to a thermal bath is no longer advised. In place it seems to be advised
>the Andersen temperature coupling with randomizatin of the velocities every
>"vrand" steps. It is suggested to avoid either too big or too small vrand
>values, but there is not a suggested value. What would be a reasonable value for
>the simulation of a protein or a peptide in explicit solvent?
>
>Thank you in advance
>
>Stefano Pieraccini
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