AMBER Archive (2008)

Subject: Re: AMBER: energy leakage?

From: David A. Case (
Date: Thu Oct 23 2008 - 06:00:29 CDT

On Thu, Oct 23, 2008, Sally Pias wrote:

> I have been
> unable to maintain constant temperature (at 300 K) upon switching from
> ntt=3 to ntt=0. In previous simulations, the temperature increased
> gradually from 298 K (after an initial dip) to 310 K over 30
> nanoseconds.

This is excessive heating, but it is hard to know the cause without knowing
what input parameters you used. Good energy conservation with ntt=0 generally
requires setting dt=0.001, tol=0.0000005 (or thereabouts), and
dsum_tol=0.000001. There may be other problems as well that can lead to
significant heating, especially if the conformation of the system is changing
during the simulation.

...good luck...dac

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