RE: Are there plans on thermostat groups?

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed May 16 2018 - 11:33:10 CDT

Wait, doesn't this already sort of exist though using tCouple and tCoupleFile? I vaguely recall once doing a tutorial demonstrating that you could set different regions of your system to different temperatures.

-Josh

On 2018-05-16 09:28:30-06:00 owner-namd-l_at_ks.uiuc.edu wrote:

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<mailto: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 Id like to test.

Best wishes
Norman Geist

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