Re: Are there plans on thermostat groups?

From: Brian Radak (brian.radak_at_gmail.com)
Date: Wed May 16 2018 - 10:24:00 CDT

Hi Norman,

No - my understanding is that this is a non-recommendable procedure and
that you are much better off rescaling forces rather than velocities in
order to reflect a different temperature in the configuration space rather
than the momentum space.

IMO It's highly unfortunate that the community continues to use the
nomenclature "solute tempering" (as in REST2) when what they really mean is
"solute scaling". The latter avoids subtle and pernicious problems with the
integration time step (you can rarely exceed 2 fs beyond 400 K!!!).

Solute scaling will be available in NAMD 2.13 (an update of the previously
reported Jo/Jiang implementation) and a less flexible version has long been
available via the "nonbondedScaling" keyword. I'm also strongly considering
dihedral based variants of the latter, since these have become somewhat
popular in the AMBER community.

Cheers,
Brian

On Wed, May 16, 2018 at 10:56 AM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:

> Hey there,
>
>
>
> Is there or will there be a possibility in NAMD to have parts of the
> system being temperature controlled to different target temperatures? This
> would be especially interesting for special REMD
>
> Protocols I’d like to test.
>
>
>
> Best wishes
>
> Norman Geist
>

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