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.
[gmx-users] 回复: 回复: Problem with Potential Mean Force calculation
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 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 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 > > 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 > > 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 > > > > Vi
[gmx-users] 回复: 回复: Problem with Potential Mean Force calculation
Dear Justin and Vu, 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 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 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 > > 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 > > 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 > >
