[gmx-users] g_wham PMF Profiles

[ZEYNEP ABALI]

Hi,

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:
https://drive.google.com/file/d/0B4ZoiZnocOaQNWVUTWU2OUxfU2s/view?usp=sharing

Histogram with all windows:

https://drive.google.com/file/d/0B4ZoiZnocOaQRFp6U05xUXI2a0E/view?usp=sharing

PMF curve with excluded windows:

https://drive.google.com/open?id=0B4ZoiZnocOaQdGpQMkpDX0V6c1E

Histogram with excluded windows:

https://drive.google.com/open?id=0B4ZoiZnocOaQQnVRMV9Zc0tDcFU


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