[gmx-users] 回复: Problem with Potential Mean Force calculation

[Rolly Ng]

Dear Justin,

I cut the x-axis to 8nm but I have uploaded the original histogram plot to
RG. Please have a look again, thank you.

I used the following command for wham,
gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal

I used the AMBER99SB-ILDN forcefield and protein protein pair is KEAP1-NRF2
(2FLU) from https://www.rcsb.org/structure/2FLU

I tried to pull the NRF2 from KEAP1, and I can visualize that it has been
successfully pulled from the initial position, producing the force and COM
plots which seem reasonable.

How can I debug the problem? Which files should I check?

Thanks,
Rolly

-----邮件原件-----
发件人: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se> 代表 Justin Lemkul
发送时间: 2020年4月21日星期二 下午7:09
收件人: Discussion list for GROMACS users <gmx-users at gromacs.org>
主题: Re: [gmx-users] Problem with Potential Mean Force calculation



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_stra
> nge_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

--
==================================================

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

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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