[gmx-users] Umbrella Sampling and histograms smoothness

Agnivo Gosai agnivogromacs14 at gmail.com
Mon Feb 9 22:11:48 CET 2015

Dear Users

My umbrella sampling simulations are of 1 ns time whereas Dr. Lemkul's
tutorial advocates a 10 ns simulation time. I found that after running WHAM
, my histograms are coarser ( rough) compared to Dr. Lemkul's. A few of my
histograms have two peaks!!
So should I increase the simulation time from 1 ns to 10 ns ?? I do a 100
ps NPT equilibration and then a 1 ns umbrella sampling in each of my
windows. The generated PMF curve is also not smooth and is discontinuous at
one position which I think I can fix by adding more windows around that

A picture is linked : ​
Kindly help.

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.

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