[gmx-users] RDF(PMF) and Umbrella sampling

Justin A. Lemkul jalemkul at vt.edu
Fri Jan 6 16:46:50 CET 2012

Gavin Melaugh wrote:
> Dear all
> I have a query regarding umbrella sampling simulations that I have
> carried out to study a dynamical process of a guest inserting into a
> host. I always get get a wall tending off to infinity at or just before
> the zero distance between the
> two species.
> The process I describe, for one system in particular, happens readily
> and I have compared the PMF from a non constrained simulation (via the
> RDF and reversible work theorem) and the same PMF from a set of 
> umbrella sampling
> simulations. They agree quite well but in the non constrained simulation
> I get a minimum practically at zero whereas for the umbrella sampling
> the minimum is shifted and there is an infinite wall close to zero. This
> wall is not present from the reversible work theorem. Why the infinite
> wall? Why does the black histogram not centre around zero. Is this an
> artefact of the umbrella technique? Please see attached the profile from
> the umbrella sampling technique, and the corresponding histograms.

What's happening is the COM reference distance is changing signs, so you get an 
artifact.  The "distance" geometry is relatively inflexible and is only suitable 
for straight pulls of continuously increasing or continuously decreasing COM 
distance.  You should try using the "position" geometry instead.  There are some 
notes that you may find useful in my tutorial:



> Here is an excerpt from one of the umbrella mdp files.
> pull        = umbrella
> pull_geometry = distance
> pull_dim = Y Y Y
> pull_start = no
> pull_ngroups = 1
> pull_group0 = cage_1
> pull_group1 = tail
> pull_init1 = 0
> pull_rate1 = 0.0
> pull_k1 = 10000
> pull_nstxout = 150
> pull_nstfout = 150
> Cheers
> Gavin
> ------------------------------------------------------------------------
> ------------------------------------------------------------------------


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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