[gmx-users] g_wham PMF Profiles

ZEYNEP ABALI zabali16 at ku.edu.tr
Fri Feb 10 08:57:18 CET 2017


I have a umbrella sampling simulation where we are pulling fragments of a
protein dimer away from each other. While selecting the windows, we have
used a 0.1 nm spacing. When I perform a g_wham by using all the windows, I
have PMF profile that is not smooth on the left hand side. But when I
exclude some of the windows, then I have a more smooth PMF profile on the
left hand side, which is more similar to what we want to have. You can find
both PMF curves and the histograms below.

PMF curve with all windows:

Histogram with all windows:


PMF curve with excluded windows:


Histogram with excluded windows:


Can you give me some insight about why this is happening?

Thank you very much for your help.

Best regards,

*Zeynep ABALI*
MSc Candidate in Biomedical Sciences and Engineering

More information about the gromacs.org_gmx-users mailing list