Re: [AMBER] vanilla Nose-Hoover thermostat availability

From: Sally Pias <>
Date: Wed, 22 Jan 2020 18:41:00 -0700

Hi Dave,

Thank you for letting me know of the plans for implementing the Bussi

I have tried the Langevin thermostat with a gamma value of 0.1 ps-1. The
effect on dynamics was far less with this setting, but I worry about the
rigor of the results. Seeing your suggestion prompts me to compare the data
we get with gamma=0.1 and with no thermostat (NVE).

Best regards,

Sally Pias
Associate Professor of Chemistry
New Mexico Tech

On Fri, Jan 17, 2020 at 7:43 AM David Case <> wrote:

> 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.
> ....dac
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Received on Wed Jan 22 2020 - 18:00:02 PST
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