Re: [gmx-users] g_wham error in umbrella simulation
On 11/8/16 9:50 AM, diana p wrote: Dear all I am doing an umbrella simulation by using the pull code in Gromacs 4.6.5 to calculate the PMF. The pull parameters are the following: ;Pull code pull= constant_force pull_geometry = position pull_dim= N N Ypull_start = no pull_ngroups = 1pull_group0 = GRApull_group1 = UNKpull_rate1 = 0.01 pull_k1 = 1000 pull_vec1 = 0.0 0.0 1.0 When i run the WHAM with the Command line: g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal it gave me the following error: Fatal error: This is not a tpr of an umbrella simulation. Found pull type "constant-force" (ir.ePull= 3) I would be more than pleased if someone could guid me. The error is pretty explicit - you didn't do umbrella sampling. You applied a constant biasing force. To do umbrella sampling, you need "pull = umbrella" in the .mdp file. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
Re: [gmx-users] g_wham error in umbrella simulation
Hi，高 发银行卡号给我，我还你钱，你结婚肯定要用钱吧 Sent from my Huawei Mobile Ming Tang m21.t...@qut.edu.au wrote: Dear all, I am doing an umbrella simulation, and come across the following error. Command line: g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000 Found 27 tpr and 27 pull force files in tpr-files.dat and pullf-files.dat, respectively Reading 13 tpr and pullf files Automatic determination of boundaries... --- Program g_wham, VERSION 5.0.4 Source code file: /home/tm/Downloads/gromacs/src/gromacs/gmxana/gmx_wham.cpp, line: 1767 Fatal error: . Should be tpr, xvg, or pdo.0.tpr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors tpr-files.dat: umbrella0.tpr umbrella137.tpr umbrella155.tpr umbrella163.tpr umbrella169.tpr umbrella174.tpr umbrella179.tpr umbrella185.tpr umbrella199.tpr umbrella206.tpr umbrella223.tpr umbrella239.tpr umbrella257.tpr umbrella275.tpr umbrella291.tpr umbrella308.tpr umbrella324.tpr umbrella344.tpr umbrella369.tpr umbrella383.tpr umbrella392.tpr umbrella422.tpr umbrella450.tpr umbrella463.tpr umbrella479.tpr umbrella497.tpr umbrella499.tpr pullf-files.dat pullf0.xvg pullf137.xvg pullf155.xvg pullf163.xvg pullf169.xvg pullf174.xvg pullf179.xvg pullf185.xvg pullf199.xvg pullf206.xvg pullf223.xvg pullf239.xvg pullf257.xvg pullf275.xvg pullf291.xvg pullf308.xvg pullf324.xvg pullf344.xvg pullf369.xvg pullf383.xvg pullf392.xvg pullf422.xvg pullf450.xvg pullf463.xvg pullf479.xvg pullf497.xvg pullf499.xvg I used this method several times before, and did not come across this problem. could anybody tell me where is the problem? Thanks -- 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.
Re: [gmx-users] g_wham error in umbrella simulation
Hi, Justin You are right. Finally, I got both of the curves. Happy! Thanks for your guidance. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Wednesday, 22 April 2015 10:18 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] g_wham error in umbrella simulation On 4/22/15 4:46 AM, Ming Tang wrote: Hi, Justin Thanks a lot. Dos2unix works. There is even no blank space in every line. The problem is that I downloaded those .dat files from the internet, which were created in windows system. But I got another problem. Following your umbrella sampling tutorial, I got the PMF curve. The trend of the curve is quite close to that of the curve in the tutorial. But, the ΔG is -31, 20 more compared to -50.5 in the tutorial. Besides, I only get one histogram, the data of the You won't get the value in the tutorial unless you follow the published protocol. The tutorial is an abbreviated version of a more complex protocol involving (1) prior simulation of 100 ns and (2) asymmetrical window distribution. I believe this should be stated already in the tutorial. rest histograms are zero (one horizontal line). Do you have any suggestions for me about what's wrong with my simulation? You're probably just not plotting the histogram file right. xmgrace -nxy histo.xvg to show all the histograms. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
Re: [gmx-users] g_wham error in umbrella simulation
Hi, Justin Thanks a lot. Dos2unix works. There is even no blank space in every line. The problem is that I downloaded those .dat files from the internet, which were created in windows system. But I got another problem. Following your umbrella sampling tutorial, I got the PMF curve. The trend of the curve is quite close to that of the curve in the tutorial. But, the ΔG is -31, 20 more compared to -50.5 in the tutorial. Besides, I only get one histogram, the data of the rest histograms are zero (one horizontal line). Do you have any suggestions for me about what's wrong with my simulation? Thank you. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Monday, 20 April 2015 10:17 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] g_wham error in umbrella simulation On 4/19/15 9:53 PM, Ming Tang wrote: Dear all, I am doing an umbrella simulation, and come across the following error. Command line: g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000 Found 27 tpr and 27 pull force files in tpr-files.dat and pullf-files.dat, respectively Reading 13 tpr and pullf files Automatic determination of boundaries... --- Program g_wham, VERSION 5.0.4 Source code file: /home/tm/Downloads/gromacs/src/gromacs/gmxana/gmx_wham.cpp, line: 1767 Fatal error: . Should be tpr, xvg, or pdo.0.tpr Is this a copy/paste problem or is this really what the line said? The error message should be Unknown file of type (something). Should be tpr, xvg, or pdo. Note the 0.tpr that is tacked on to the end and the lack of preceding text. Any weird line endings in your tpr-files.dat file? Check and run dos2unix if needed. The presence of 0.tpr somewhat suggests the very first line is causing a problem, even though it appears gmx wham understands how many files it should find; it just can't determine the right file names/types. -Justin For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors tpr-files.dat: umbrella0.tpr umbrella137.tpr umbrella155.tpr umbrella163.tpr umbrella169.tpr umbrella174.tpr umbrella179.tpr umbrella185.tpr umbrella199.tpr umbrella206.tpr umbrella223.tpr umbrella239.tpr umbrella257.tpr umbrella275.tpr umbrella291.tpr umbrella308.tpr umbrella324.tpr umbrella344.tpr umbrella369.tpr umbrella383.tpr umbrella392.tpr umbrella422.tpr umbrella450.tpr umbrella463.tpr umbrella479.tpr umbrella497.tpr umbrella499.tpr pullf-files.dat pullf0.xvg pullf137.xvg pullf155.xvg pullf163.xvg pullf169.xvg pullf174.xvg pullf179.xvg pullf185.xvg pullf199.xvg pullf206.xvg pullf223.xvg pullf239.xvg pullf257.xvg pullf275.xvg pullf291.xvg pullf308.xvg pullf324.xvg pullf344.xvg pullf369.xvg pullf383.xvg pullf392.xvg pullf422.xvg pullf450.xvg pullf463.xvg pullf479.xvg pullf497.xvg pullf499.xvg I used this method several times before, and did not come across this problem. could anybody tell me where is the problem? Thanks -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
Re: [gmx-users] g_wham error in umbrella simulation
On 4/22/15 4:46 AM, Ming Tang wrote: Hi, Justin Thanks a lot. Dos2unix works. There is even no blank space in every line. The problem is that I downloaded those .dat files from the internet, which were created in windows system. But I got another problem. Following your umbrella sampling tutorial, I got the PMF curve. The trend of the curve is quite close to that of the curve in the tutorial. But, the ΔG is -31, 20 more compared to -50.5 in the tutorial. Besides, I only get one histogram, the data of the You won't get the value in the tutorial unless you follow the published protocol. The tutorial is an abbreviated version of a more complex protocol involving (1) prior simulation of 100 ns and (2) asymmetrical window distribution. I believe this should be stated already in the tutorial. rest histograms are zero (one horizontal line). Do you have any suggestions for me about what's wrong with my simulation? You're probably just not plotting the histogram file right. xmgrace -nxy histo.xvg to show all the histograms. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
Re: [gmx-users] g_wham error in umbrella simulation
On 4/19/15 9:53 PM, Ming Tang wrote: Dear all, I am doing an umbrella simulation, and come across the following error. Command line: g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000 Found 27 tpr and 27 pull force files in tpr-files.dat and pullf-files.dat, respectively Reading 13 tpr and pullf files Automatic determination of boundaries... --- Program g_wham, VERSION 5.0.4 Source code file: /home/tm/Downloads/gromacs/src/gromacs/gmxana/gmx_wham.cpp, line: 1767 Fatal error: . Should be tpr, xvg, or pdo.0.tpr Is this a copy/paste problem or is this really what the line said? The error message should be Unknown file of type (something). Should be tpr, xvg, or pdo. Note the 0.tpr that is tacked on to the end and the lack of preceding text. Any weird line endings in your tpr-files.dat file? Check and run dos2unix if needed. The presence of 0.tpr somewhat suggests the very first line is causing a problem, even though it appears gmx wham understands how many files it should find; it just can't determine the right file names/types. -Justin For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors tpr-files.dat: umbrella0.tpr umbrella137.tpr umbrella155.tpr umbrella163.tpr umbrella169.tpr umbrella174.tpr umbrella179.tpr umbrella185.tpr umbrella199.tpr umbrella206.tpr umbrella223.tpr umbrella239.tpr umbrella257.tpr umbrella275.tpr umbrella291.tpr umbrella308.tpr umbrella324.tpr umbrella344.tpr umbrella369.tpr umbrella383.tpr umbrella392.tpr umbrella422.tpr umbrella450.tpr umbrella463.tpr umbrella479.tpr umbrella497.tpr umbrella499.tpr pullf-files.dat pullf0.xvg pullf137.xvg pullf155.xvg pullf163.xvg pullf169.xvg pullf174.xvg pullf179.xvg pullf185.xvg pullf199.xvg pullf206.xvg pullf223.xvg pullf239.xvg pullf257.xvg pullf275.xvg pullf291.xvg pullf308.xvg pullf324.xvg pullf344.xvg pullf369.xvg pullf383.xvg pullf392.xvg pullf422.xvg pullf450.xvg pullf463.xvg pullf479.xvg pullf497.xvg pullf499.xvg I used this method several times before, and did not come across this problem. could anybody tell me where is the problem? Thanks -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
Re: [gmx-users] g_wham error in umbrella simulation
Thanks for your advice. I just checked. There is no empty line at the end of the .dat files. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Kortzak, Daniel Sent: Monday, 20 April 2015 8:01 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] g_wham error in umbrella simulation Maybe some empty lines at the end of your .dat files. Dear all, I am doing an umbrella simulation, and come across the following error. Command line: g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000 Found 27 tpr and 27 pull force files in tpr-files.dat and pullf-files.dat, respectively Reading 13 tpr and pullf files Automatic determination of boundaries... --- Program g_wham, VERSION 5.0.4 Source code file: /home/tm/Downloads/gromacs/src/gromacs/gmxana/gmx_wham.cpp, line: 1767 Fatal error: . Should be tpr, xvg, or pdo.0.tpr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors tpr-files.dat: umbrella0.tpr umbrella137.tpr umbrella155.tpr umbrella163.tpr umbrella169.tpr umbrella174.tpr umbrella179.tpr umbrella185.tpr umbrella199.tpr umbrella206.tpr umbrella223.tpr umbrella239.tpr umbrella257.tpr umbrella275.tpr umbrella291.tpr umbrella308.tpr umbrella324.tpr umbrella344.tpr umbrella369.tpr umbrella383.tpr umbrella392.tpr umbrella422.tpr umbrella450.tpr umbrella463.tpr umbrella479.tpr umbrella497.tpr umbrella499.tpr pullf-files.dat pullf0.xvg pullf137.xvg pullf155.xvg pullf163.xvg pullf169.xvg pullf174.xvg pullf179.xvg pullf185.xvg pullf199.xvg pullf206.xvg pullf223.xvg pullf239.xvg pullf257.xvg pullf275.xvg pullf291.xvg pullf308.xvg pullf324.xvg pullf344.xvg pullf369.xvg pullf383.xvg pullf392.xvg pullf422.xvg pullf450.xvg pullf463.xvg pullf479.xvg pullf497.xvg pullf499.xvg I used this method several times before, and did not come across this problem. could anybody tell me where is the problem? Thanks Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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.
Re: [gmx-users] g_wham error in umbrella simulation
Dear Mr. Kortzak, I had same problems. There could be many reasons, but in my case, I had some uncompleted jobs. For instance, umbrella137 could be terminated abnormally but you can have tpr, log and xvg which are generated from uncompleted job. Why don’t you check the results? Regards Yoochan On Apr 20, 2015, at 7:01 PM, Kortzak, Daniel d.kort...@fz-juelich.de wrote: Maybe some empty lines at the end of your .dat files. Dear all, I am doing an umbrella simulation, and come across the following error. Command line: g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000 Found 27 tpr and 27 pull force files in tpr-files.dat and pullf-files.dat, respectively Reading 13 tpr and pullf files Automatic determination of boundaries... --- Program g_wham, VERSION 5.0.4 Source code file: /home/tm/Downloads/gromacs/src/gromacs/gmxana/gmx_wham.cpp, line: 1767 Fatal error: . Should be tpr, xvg, or pdo.0.tpr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors tpr-files.dat: umbrella0.tpr umbrella137.tpr umbrella155.tpr umbrella163.tpr umbrella169.tpr umbrella174.tpr umbrella179.tpr umbrella185.tpr umbrella199.tpr umbrella206.tpr umbrella223.tpr umbrella239.tpr umbrella257.tpr umbrella275.tpr umbrella291.tpr umbrella308.tpr umbrella324.tpr umbrella344.tpr umbrella369.tpr umbrella383.tpr umbrella392.tpr umbrella422.tpr umbrella450.tpr umbrella463.tpr umbrella479.tpr umbrella497.tpr umbrella499.tpr pullf-files.dat pullf0.xvg pullf137.xvg pullf155.xvg pullf163.xvg pullf169.xvg pullf174.xvg pullf179.xvg pullf185.xvg pullf199.xvg pullf206.xvg pullf223.xvg pullf239.xvg pullf257.xvg pullf275.xvg pullf291.xvg pullf308.xvg pullf324.xvg pullf344.xvg pullf369.xvg pullf383.xvg pullf392.xvg pullf422.xvg pullf450.xvg pullf463.xvg pullf479.xvg pullf497.xvg pullf499.xvg I used this method several times before, and did not come across this problem. could anybody tell me where is the problem? Thanks Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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.
