AMBER Archive (2006)

Subject: AMBER: temperature regulation

From: Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Stefano.Pieraccini_at_unimi.it)
Date: Tue Jul 18 2006 - 03:31:04 CDT

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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