[gmx-users] PMF - US histograms problem

Sajeewa Pemasinghe sajeewasp at gmail.com
Mon Mar 27 15:09:45 CEST 2017


When I get  a region sparsely populated like that, I increase the number of
points in that particular region and increase the k value to about 3000 but
not more than that. Increasing the k value to something like 20000 will
result in the distribution getting very narrow and therefore further
hindering the overlap. It could also be that the coordinate(path) you have
chosen is not a good one to pull the peptide out. Changing the
pull_geometry from distance to cylinder might also help as used in this




On Mon, Mar 27, 2017 at 1:50 PM, Eudes Fileti <fileti at gmail.com> wrote:

> Hi everyone, I'm trying to calculate the PMF for the extraction of a
> peptide from within a peptide nanostructure. However I'm having difficulty
> to overlap the histograms for the first pulling windows: Many full overlap
> windows follow by a large gap with no histogram.
> I've tried the two things I could: reduce the distance increment between
> the windows (now I'm using 0.05nm), and I've already done several tests
> with different force constants with k up to 20000! For each window test I
> run only 1ns of sampling.
> Anyone have any suggestions? Could another umbrella sampling scheme
> (constraint pulling) be more efficient in this case?
> Bests
> _______________________________________
> Eudes Eterno Fileti
> Instituto de Ciência e Tecnologia da UNIFESP
> Av. Cesar Lattes, 1201, Eugênio de Mello, SP, 12247-014
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