Re: [gmx-users] Problem using gmx wham
Hi Justin, Thanks for your response. I've attempted to run gmx wham using GROMACS 5.1.4 and I seem to get the same problem, even if I attempt to use dos2unix before I issue a command i.e. --- Program gmx wham, VERSION 5.1.4 Source code file: /local/software/gromacs/5.1.4/source/gromacs-5.1.4/src/gromacs/gmxana/gmx_wham.cpp, line: 1800 Fatal error: Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I've taken a look at older posts relating to this problem, and I saw that a similar complaint was resolved after the poster used dos2unix (following your recommendation). But that hasn't seemed to work for me. Regards, From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Tuesday, November 14, 2017 2:35 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Problem using gmx wham At least upgrade to the latest release in the series (5.1.4) or better yet, the actual latest version (2016.4) to see if this is a bug that's been fixed. I seem to recall this same behavior reported before and subsequently solved, but haven't dug it up. -Justin On 11/13/17 7:11 AM, Jefferies D.F. wrote: > Hey guys, > > Sorry if it seems that I'm bumping this thread, but I was wondering if anyone > had any other suggestions before I let this thread die. > > Thanks. > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Jefferies > D.F. [dfj1...@soton.ac.uk] > Sent: Thursday, November 02, 2017 1:29 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Problem using gmx wham > > Hi Justin, > > Thanks for the response. The .dat files were created with the vi text editor, > they contain lists of the .tpr and .xvg to be read, e.g. > > umbrella0.tpr > umbrella1.tpr > umbrella2.tpr > .. > umbrella52.tpr > > I've tried to use dos2unix, i.e. > ~> dos2unix tpr-files.dat > and > ~> dos2unix pullf-files.dat > > but I still get the same error message i.e. > > --- > Program gmx wham, VERSION 5.1.2 > Source code file: > /Users/Damien/Downloads/gromacs-5.1.2/src/gromacs/gmxana/gmx_wham.cpp, line: > 1800 > > Fatal error: > Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo. > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > --- > > That being said, it seems you're correct in thinking something's weird with > the input files. After I created new .dat files, I got this message: > > --- > Program gmx wham, VERSION 5.1.2 > Source code file: > /Users/Damien/Downloads/gromacs-5.1.2/src/gromacs/gmxana/gmx_wham.cpp, line: > 3610 > > Fatal error: > Found 53 file names in tpr-files.dat, but 54 in pullf-files.dat > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > --- > > gmx wham is registering 54 files, when only 53 were written. > > > > > > ____ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin > Lemkul [jalem...@vt.edu] > Sent: Thursday, November 02, 2017 11:10 AM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Problem using gmx wham > > On 11/1/17 4:26 PM, Jefferies D.F. wrote: >> Hi, >> >> I am attempting to use gmx wham to compute a potential of mean force. I have >> used the command line: >> >> gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kJ >> >> where tpr-files.dat and pullf-files.dat contain a list of the .tpr and >> pullf.xvg files from each umbrella sampling window, respectively. >> >> It seems that gmx wham is having trouble reading the .tpr and .xvg files, as >> I get this error message: >> >> --- >> >> Program gmx wham, VERSION 5.1.4 >> >> Source code file: >> /local/software/gromacs/5.1.4/source/gromacs-5.1.4/src/gromacs/gmxana/gmx_wham.c
Re: [gmx-users] Problem using gmx wham
At least upgrade to the latest release in the series (5.1.4) or better yet, the actual latest version (2016.4) to see if this is a bug that's been fixed. I seem to recall this same behavior reported before and subsequently solved, but haven't dug it up. -Justin On 11/13/17 7:11 AM, Jefferies D.F. wrote: Hey guys, Sorry if it seems that I'm bumping this thread, but I was wondering if anyone had any other suggestions before I let this thread die. Thanks. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Jefferies D.F. [dfj1...@soton.ac.uk] Sent: Thursday, November 02, 2017 1:29 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Problem using gmx wham Hi Justin, Thanks for the response. The .dat files were created with the vi text editor, they contain lists of the .tpr and .xvg to be read, e.g. umbrella0.tpr umbrella1.tpr umbrella2.tpr .. umbrella52.tpr I've tried to use dos2unix, i.e. ~> dos2unix tpr-files.dat and ~> dos2unix pullf-files.dat but I still get the same error message i.e. --- Program gmx wham, VERSION 5.1.2 Source code file: /Users/Damien/Downloads/gromacs-5.1.2/src/gromacs/gmxana/gmx_wham.cpp, line: 1800 Fatal error: Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- That being said, it seems you're correct in thinking something's weird with the input files. After I created new .dat files, I got this message: --- Program gmx wham, VERSION 5.1.2 Source code file: /Users/Damien/Downloads/gromacs-5.1.2/src/gromacs/gmxana/gmx_wham.cpp, line: 3610 Fatal error: Found 53 file names in tpr-files.dat, but 54 in pullf-files.dat For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- gmx wham is registering 54 files, when only 53 were written. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Thursday, November 02, 2017 11:10 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Problem using gmx wham On 11/1/17 4:26 PM, Jefferies D.F. wrote: Hi, I am attempting to use gmx wham to compute a potential of mean force. I have used the command line: gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kJ where tpr-files.dat and pullf-files.dat contain a list of the .tpr and pullf.xvg files from each umbrella sampling window, respectively. It seems that gmx wham is having trouble reading the .tpr and .xvg files, as I get this error message: --- Program gmx wham, VERSION 5.1.4 Source code file: /local/software/gromacs/5.1.4/source/gromacs-5.1.4/src/gromacs/gmxana/gmx_wham.cpp, line: 1800 Fatal error: Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo. The extra space after "tpr" in the printed error suggests something is weird with the input .dat file. Did you create it with a proper plain text editor? What about running dos2unix on it to make sure you've got the right kind of line endings? -Justin For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I have computed potential of mean force profiles before (using this Mac), but I haven't encountered this problem. Could someone help me with this problem? -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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/grom
Re: [gmx-users] Problem using gmx wham
Hey guys, Sorry if it seems that I'm bumping this thread, but I was wondering if anyone had any other suggestions before I let this thread die. Thanks. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Jefferies D.F. [dfj1...@soton.ac.uk] Sent: Thursday, November 02, 2017 1:29 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Problem using gmx wham Hi Justin, Thanks for the response. The .dat files were created with the vi text editor, they contain lists of the .tpr and .xvg to be read, e.g. umbrella0.tpr umbrella1.tpr umbrella2.tpr .. umbrella52.tpr I've tried to use dos2unix, i.e. ~> dos2unix tpr-files.dat and ~> dos2unix pullf-files.dat but I still get the same error message i.e. --- Program gmx wham, VERSION 5.1.2 Source code file: /Users/Damien/Downloads/gromacs-5.1.2/src/gromacs/gmxana/gmx_wham.cpp, line: 1800 Fatal error: Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- That being said, it seems you're correct in thinking something's weird with the input files. After I created new .dat files, I got this message: --- Program gmx wham, VERSION 5.1.2 Source code file: /Users/Damien/Downloads/gromacs-5.1.2/src/gromacs/gmxana/gmx_wham.cpp, line: 3610 Fatal error: Found 53 file names in tpr-files.dat, but 54 in pullf-files.dat For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- gmx wham is registering 54 files, when only 53 were written. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Thursday, November 02, 2017 11:10 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Problem using gmx wham On 11/1/17 4:26 PM, Jefferies D.F. wrote: > Hi, > > I am attempting to use gmx wham to compute a potential of mean force. I have > used the command line: > > gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kJ > > where tpr-files.dat and pullf-files.dat contain a list of the .tpr and > pullf.xvg files from each umbrella sampling window, respectively. > > It seems that gmx wham is having trouble reading the .tpr and .xvg files, as > I get this error message: > > --- > > Program gmx wham, VERSION 5.1.4 > > Source code file: > /local/software/gromacs/5.1.4/source/gromacs-5.1.4/src/gromacs/gmxana/gmx_wham.cpp, > line: 1800 > > > Fatal error: > > Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo. > The extra space after "tpr" in the printed error suggests something is weird with the input .dat file. Did you create it with a proper plain text editor? What about running dos2unix on it to make sure you've got the right kind of line endings? -Justin > For more information and tips for troubleshooting, please check the GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > --- > > > I have computed potential of mean force profiles before (using this Mac), but > I haven't encountered this problem. Could someone help me with this problem? > > -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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. -- Gromacs Users mailing list * Please search the archive at http://www.grom
Re: [gmx-users] Problem using gmx wham
Hi Justin, Thanks for the response. The .dat files were created with the vi text editor, they contain lists of the .tpr and .xvg to be read, e.g. umbrella0.tpr umbrella1.tpr umbrella2.tpr .. umbrella52.tpr I've tried to use dos2unix, i.e. ~> dos2unix tpr-files.dat and ~> dos2unix pullf-files.dat but I still get the same error message i.e. --- Program gmx wham, VERSION 5.1.2 Source code file: /Users/Damien/Downloads/gromacs-5.1.2/src/gromacs/gmxana/gmx_wham.cpp, line: 1800 Fatal error: Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- That being said, it seems you're correct in thinking something's weird with the input files. After I created new .dat files, I got this message: --- Program gmx wham, VERSION 5.1.2 Source code file: /Users/Damien/Downloads/gromacs-5.1.2/src/gromacs/gmxana/gmx_wham.cpp, line: 3610 Fatal error: Found 53 file names in tpr-files.dat, but 54 in pullf-files.dat For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- gmx wham is registering 54 files, when only 53 were written. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Thursday, November 02, 2017 11:10 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Problem using gmx wham On 11/1/17 4:26 PM, Jefferies D.F. wrote: > Hi, > > I am attempting to use gmx wham to compute a potential of mean force. I have > used the command line: > > gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kJ > > where tpr-files.dat and pullf-files.dat contain a list of the .tpr and > pullf.xvg files from each umbrella sampling window, respectively. > > It seems that gmx wham is having trouble reading the .tpr and .xvg files, as > I get this error message: > > --- > > Program gmx wham, VERSION 5.1.4 > > Source code file: > /local/software/gromacs/5.1.4/source/gromacs-5.1.4/src/gromacs/gmxana/gmx_wham.cpp, > line: 1800 > > > Fatal error: > > Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo. > The extra space after "tpr" in the printed error suggests something is weird with the input .dat file. Did you create it with a proper plain text editor? What about running dos2unix on it to make sure you've got the right kind of line endings? -Justin > For more information and tips for troubleshooting, please check the GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > --- > > > I have computed potential of mean force profiles before (using this Mac), but > I haven't encountered this problem. Could someone help me with this problem? > > -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] Problem using gmx wham
On 11/1/17 4:26 PM, Jefferies D.F. wrote: Hi, I am attempting to use gmx wham to compute a potential of mean force. I have used the command line: gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kJ where tpr-files.dat and pullf-files.dat contain a list of the .tpr and pullf.xvg files from each umbrella sampling window, respectively. It seems that gmx wham is having trouble reading the .tpr and .xvg files, as I get this error message: --- Program gmx wham, VERSION 5.1.4 Source code file: /local/software/gromacs/5.1.4/source/gromacs-5.1.4/src/gromacs/gmxana/gmx_wham.cpp, line: 1800 Fatal error: Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo. The extra space after "tpr" in the printed error suggests something is weird with the input .dat file. Did you create it with a proper plain text editor? What about running dos2unix on it to make sure you've got the right kind of line endings? -Justin For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I have computed potential of mean force profiles before (using this Mac), but I haven't encountered this problem. Could someone help me with this problem? -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] Problem using gmx wham
Hi, I am attempting to use gmx wham to compute a potential of mean force. I have used the command line: gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kJ where tpr-files.dat and pullf-files.dat contain a list of the .tpr and pullf.xvg files from each umbrella sampling window, respectively. It seems that gmx wham is having trouble reading the .tpr and .xvg files, as I get this error message: --- Program gmx wham, VERSION 5.1.4 Source code file: /local/software/gromacs/5.1.4/source/gromacs-5.1.4/src/gromacs/gmxana/gmx_wham.cpp, line: 1800 Fatal error: Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I have computed potential of mean force profiles before (using this Mac), but I haven't encountered this problem. Could someone help me with this problem? -- 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.