[gmx-users] H-REMD in umbrella sampling
jalemkul at vt.edu
Tue Nov 24 19:44:09 CET 2015
On 11/24/15 12:06 PM, adam wrote:
> Thank you for the advice. Though, I am a bit confused how one could implement
> such particles in practice. What do you understand by “make two virtual
> particles” ? Where it should be defined in gromacs inputs ?
> Also, as I understand, if I run standard umbrella sampling simulation with
> the pulling code in gromacs, it is already using such approach (COM pulling).
> I suppose that the issue here is how to force gromacs to treat different
> distances between COMs (and therefore different pulling potential leading to
> different Hamiltonian) as an argument for REMD (H-REMD in this case) and
> perform exchange between the umbrella windows.
Indeed the virtual particle suggestion is unnecessary. The pull code does this
without any extra particles. The only element of the pull code that can be
modulated is the force constant for the biasing force (pull-coord*-k and
pull-coord*-kB), which is changed as a function of lambda and according to
restraint-lambdas. If the goal is any other type of lambda-dependent
transformation (the reaction coordinate, the restraint length, etc), to my
knowledge, it doesn't exist in GROMACS.
> Since there is no answer from gromacs developers I assume that the above is
> not yet implemented and based on the http://redmine.gromacs.org/issues/1335
> <http://redmine.gromacs.org/issues/1335> the implementation is postponed for
> the “future”. Thus, anyone trying to use such feature should look for
> solution elsewhere.
> Thank you.
> Best regards, Adam
>> On 23 Nov 2015, at 17:12, Yuri Garmay <yuri.from.spb at gmail.com> wrote:
>> One can make two virtual particles at COMs of corresponding molecules and
>> set harmonic potential between them with different length for lambdas 0 and
>> -- Best regards, Yuri -- Gromacs Users mailing list
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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