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

Gavin Melaugh gmelaugh01 at qub.ac.uk
Fri Jan 6 16:39:01 CET 2012

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.

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


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