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 ================================================== -- 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. -- 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.