On 4/21/20 2:08 AM, Rolly Ng wrote:

Dear Gromacs user and Dr. lemkul,

I think my previous email is too large to send on the list. Could you please kindly look at the link for the plots?


I don't see how the PMF could possibly arise from your data. The reaction coordinate extends from 2 - 6 nm, but your PMF plot goes from 0 - 10 nm.

I tried to applied the umbrella tutorial to my protein-protein system, and I am using GROMACS 2020


I have very dense windows to 0.1nm as shown on the attached histogram, but as I look at the PMF curve, it is strange and incomplete?

I hope you're not directly applying the tutorial; there are some aspects of it (use of restraints, the window spacing, and the restraint only along z) that are not applicable to general protein-protein complexes.

Could you please help me to check what has gone wrong?

What was your gmx wham command? I really don't understand how it could have even produced that PMF given the data you have in the histograms.



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129


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