Re: [AMBER] vanilla Nose-Hoover thermostat availability

From: David Case <>
Date: Fri, 17 Jan 2020 14:43:07 +0000

On Thu, Jan 16, 2020, Sally Pias wrote:
>It is my impression that the "vanilla" Nose-Hoover thermostat is not
>available in Amber. If that is correct, is there any intention of
>implementing it? Its availability would greatly benefit membrane permeation
>studies, as Langevin temperature control dampens dynamics and the Berendsen
>weak-coupling thermostat tends to distribute the temperature unevenly.

I don't know of any such plans, but others may chime in. Amber20 will
have a new implementation of the "Bussi" thermostat, which makes (with
appropriate parameter choices) minimal disruption of dynamics.

Also, just checking about whether you have used a Langevin thermostat
with a very small value for gamma_ln (say something like 0.1)? I don't
have experience with membrane permeation simulations, but in other
circumstances, dampening of dynamics is highly dependent on gamma_ln.


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Received on Fri Jan 17 2020 - 07:00:03 PST
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