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 ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.