Dear Justin,

Please refer to my figures on RG,
https://www.researchgate.net/post/GROMACS_2020_pull_code_produces_strange_Po
tential_Mean_Force_PMF_result

The 1st plot of my question shows the pull force of the Steered MD of 500
ps, and I have visualized that the guest was gradually moved away from the
host.

By looking at the pull force, I suppose that the frames from 0 to about 250
ps are sufficient for the umbrella sampling and your tutorial was 0 to 160
ps. So, I suppose only the linear section of the pull force frames are need.
When I was checking the tpr/xvg pairs, instead of using all frames, I
reduced the umber of file pairs to 27. Whereas the 51 pairs are for the
entire 500 ps.

Thank you very much for your patient and I have also updated my answer on RG
with two new plots showing the PMF (free_energy.png) and histogram
(histo.png) from 0 to 5 nm.

Regards,
Rolly

-----邮件原件-----
发件人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> 代表 Justin Lemkul
发送时间: 2020年4月23日星期四 下午6:17
收件人: gmx-us...@gromacs.org
主题: Re: [gmx-users] 回复: 回复: Problem with Potential Mean Force
calculation



On 4/22/20 10:40 AM, Rolly Ng wrote:
> Dear Justin and Vu,
>
> I think I have solved part of my problem. The number of tpr/xvg pairs were
too much in my case. Although I used the script to generate 50 pairs with 0.
1nm setting, it turns out that only the first 27 pairs works.

What does "only the first 27 pairs work" mean?

> ./setupUmbrella.py summary_distances.dat 0.1 run-umbrella.sh &> 
> caught-output.txt
>
> Please find my summary_distances.dat and caught-output.txt attached.
>
> I also found that the wham loops for very long time if there is problem
with the tpr/xvg pairs. A normal run will last only tens of iteration. I
have to check the pairs one by one in order to get a reasonable PMF. I have
uploaded them to RG.
>
> What could be the problem with the tpr/xvg pairs? How can I avoid it the
next time?

The reaction coordinate you established with these 51 .tpr files is
consistent with the histograms you showed - sampling roughly between 2 -
8 nm. The PMF is still basically an impossibility based on these data.

-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

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

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

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