From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu May 17 2018 - 02:25:49 CDT
Thanks for your answers. I will look into how far I can get with my implementation of a REST2 style sampling, what you apparently already concluded ;)
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Brian Radak
Gesendet: Mittwoch, 16. Mai 2018 19:52
An: Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
Cc: norman.geist_at_uni-greifswald.de; namd-l_at_ks.uiuc.edu
Betreff: Re: namd-l: Are there plans on thermostat groups?
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 <mailto: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.
On 2018-05-16 09:28:30-06:00 owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu> wrote:
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.
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:
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.
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2019 - 23:19:56 CST