AMBER Archive (2005)

Subject: Re: AMBER: Andersen thermostat: target T?

From: David A. Case (case_at_scripps.edu)
Date: Fri Jan 21 2005 - 18:23:17 CST

On Fri, Jan 21, 2005, Arantxa Sanz wrote:
>
> I have been running the following Sander script to run MD dynamics at
> constant T with Andersen thermostat
> Discarding the first 200ps, it seems that average T oscillates
> around 310K. That is, 10K above the given target T.

Try setting vrand to a lower value than its default value of 1000. Also,
run some tests with a small value of ntpr and look closely at the temperature
profile....maybe that will give some hints.

Also: be sure that you really want/need this sort of thermostat. It is
implemented in only a very naive way.

...dac

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