[gmx-users] Problem with Potential Mean Force calculation

[Justin Lemkul]

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?
>
> https://www.researchgate.net/post/GROMACS_2020_pull_code_produces_strange_Potential_Mean_Force_PMF_result
>

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
>
> http://www.mdtutorials.com/gmx/umbrella/index.html
>
> 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

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
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