[gmx-users] PMF - US histograms problem

Eudes Fileti fileti at gmail.com
Mon Mar 27 11:50:49 CEST 2017

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?

Eudes Eterno Fileti
Instituto de Ciência e Tecnologia da UNIFESP
Av. Cesar Lattes, 1201, Eugênio de Mello, SP, 12247-014

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