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 Cheers Gavin
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