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 &> 

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 

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 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


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