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

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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