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

[Justin Lemkul]

On 4/21/20 10:40 AM, Rolly Ng wrote:
> 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.

It's not a matter of changing the axis. Your histograms indicate 
sampling from 2 - 8 nm. Your PMF is computed from 0 - 10 nm. If you have 
a protein-protein complex, I doubt the COM distance can ever be zero. 
There is a disconnect between your files.

-Justin

> 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
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
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-- 
==================================================

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

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================