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. ./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? Thanks, Rolly Thank you and I am checking the tpr and vxg files by reducing the number of files in the 2 dat files. The first 10 data points seems giving the correct PMF reading although the list is incomplete, so I suspect that some of my tpr and xvg files are bad for wham. I will report my finding after check all 51 tpr/vxg pairs. Thank you, 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 Quyen V. Vu 发送时间: 2020年4月21日星期二 下午11:10 收件人: gmx-us...@gromacs.org 主题: Re: [gmx-users] 回复: Problem with Potential Mean Force calculation I think the output from WHAM in the terminal may give some information to detect the problem. WHAM will tell you the boundary he used to fit your PMF because your histogram and COM position both tell us your reaction coordinate is range from about 2-7nm but WHAM fit from 0-10nm is so strange Best regards, On Tue, Apr 21, 2020 at 4:49 PM Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/21/20 10:40 AM, Rolly Ng wrote: > > 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. > > It's not a matter of changing the axis. Your histograms indicate > sampling from 2 - 8 nm. Your PMF is computed from 0 - 10 nm. If you > have a protein-protein complex, I doubt the COM distance can ever be zero. > There is a disconnect between your files. > > -Justin > > > 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_s > >> tra 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. > > > > -- > ================================================== > > 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? 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Creating frame-specific output for files: run-umbrella.sh frame dist d_dist 0 2.233 NA 59 2.333 0.100 87 2.435 0.102 116 2.532 0.097 130 2.633 0.101 142 2.737 0.104 167 2.838 0.101 183 2.933 0.095 190 3.034 0.101 192 3.156 0.122 196 3.255 0.099 200 3.363 0.108 203 3.500 0.137 206 3.596 0.096 210 3.712 0.116 213 3.797 0.085 217 3.866 0.069 219 3.993 0.127 223 4.078 0.085 226 4.194 0.116 230 4.306 0.112 237 4.408 0.102 244 4.523 0.115 247 4.605 0.082 256 4.699 0.094 264 4.794 0.095 272 4.888 0.094 278 5.001 0.113 285 5.102 0.101 296 5.192 0.090 304 5.277 0.085 323 5.382 0.105 329 5.476 0.094 332 5.574 0.098 347 5.682 0.108 354 5.790 0.108 367 5.891 0.101 376 5.984 0.093 388 6.088 0.104 391 6.172 0.084 394 6.272 0.100 414 6.363 0.091 427 6.463 0.100 436 6.565 0.102 441 6.663 0.098 446 6.754 0.091 465 6.865 0.111 473 6.961 0.096 486 7.061 0.100 493 7.161 0.100 494 7.181 0.020
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