Dear Justin, I cut the x-axis to 8nm but I have uploaded the original histogram plot to RG. Please have a look again, thank you.
I used the following command for wham, gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal I used the AMBER99SB-ILDN forcefield and protein protein pair is KEAP1-NRF2 (2FLU) from https://www.rcsb.org/structure/2FLU I tried to pull the NRF2 from KEAP1, and I can visualize that it has been successfully pulled from the initial position, producing the force and COM plots which seem reasonable. How can I debug the problem? Which files should I check? Thanks, 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21日星期二 下午7:09 收件人: Discussion list for GROMACS users <gmx-us...@gromacs.org> 主题: Re: [gmx-users] Problem with Potential Mean Force calculation On 4/21/20 2:08 AM, Rolly Ng wrote: > > Dear Gromacs user and Dr. lemkul, > > I think my previous email is too large to send on the list. Could you > please kindly look at the link for the plots? > > https://www.researchgate.net/post/GROMACS_2020_pull_code_produces_stra > nge_Potential_Mean_Force_PMF_result > I don't see how the PMF could possibly arise from your data. The reaction coordinate extends from 2 - 6 nm, but your PMF plot goes from 0 - 10 nm. > I tried to applied the umbrella tutorial to my protein-protein system, > and I am using GROMACS 2020 > > http://www.mdtutorials.com/gmx/umbrella/index.html > > I have very dense windows to 0.1nm as shown on the attached histogram, > but as I look at the PMF curve, it is strange and incomplete? > I hope you're not directly applying the tutorial; there are some aspects of it (use of restraints, the window spacing, and the restraint only along z) that are not applicable to general protein-protein complexes. > Could you please help me to check what has gone wrong? > What was your gmx wham command? I really don't understand how it could have even produced that PMF given the data you have in the histograms. -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.