Re: Are there plans on thermostat groups?

From: Brian Radak (brian.radak_at_gmail.com)
Date: Wed May 16 2018 - 12:52:09 CDT

That's true, but tCouple is essentially Berendsen style rescaling, which
probably isn't useful for most applications. You can also do
non-homogeneous friction coefficients for Langevin dynamics via PDB
selections. Both of those might cause performance problems in the future.

On Wed, May 16, 2018 at 12:33 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> 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> 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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