Recover the PMF along an unbiased CV

From: Felipe Merino (
Date: Thu Jan 14 2016 - 16:11:37 CST

Dear all,

This is a slightly off topic question, but I had a small doubt which I
know somebody there can help me with. I have some umbrella sampling
simulations with the bias applied to a specific set of atoms. I'd like
to know now the PMF along a slightly different CV. Since both are highly
correlated, the biasing on one pretty much allows me to explore the second.

In my understanding, this should not be a problem given that I know the
value of both CVs for each point, and therefore I can keep track of the
bias on the system, and perform the re-weighting of the trajectories
based on the new CV and it's associated bias. Of course, the histograms
are rather noisy and the PMF looks a bit ugly, but it quite matches what
I was expecting.

Am I missing something here or does this sound correct?

I'd appreciate a lot some comments on the topic.



Felipe Merino
Max Planck Institute for Molecular Physiology
Department of Structural Biochemistry
Otto-Hahn-Str. 11
44227 Dortmund
Phone: +49 231 133 2306

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