Re: [gmx-users] which tool to use a measure a user-defined angle in a traj
ok. I'll give it a shot too, should get the same answer , will be a good way to double check, Arneh Alan Dodd wrote: Fair enough, but I'll just repeat that g_bundle does *exactly* what you want in your example - provide it with an index file with two groups with the COMs defining the ends of the axes (in your case, one C in one group and one O in the other) and the option -z, and it'll dump out a file of the angle those axes make with the z-axis. Don't be put off by the way it appears to be designed for helices. - Original Message From: Arneh Babakhani <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Tuesday, July 17, 2007 1:30:22 AM Subject: Re: [gmx-users] which tool to use a measure a user-defined angle in a traj ok, thanks. I like Chris's suggestion. I'll try using matlab to parse it out (b/c matlab can easily ingest column formatted data), Arneh Tsjerk Wassenaar wrote: Hi Arneh, I think you're out of luck here. However, this is an excellent exercise to get started with writing custom made analysis tools :) Alternatively, you could output the coordinates for the C and O using g_traj and use a script to calculate the angles with the z-axis, in case it's a single bond you're interested in. Cheers, Tsjerk On 7/13/07, Arneh Babakhani <[EMAIL PROTECTED]> wrote: Hi, Looking through the gmx tools . . . was wondering, which tool would one use (if such a tool exists) to measure the fluctuation of a user-defined angle in a trajectory. For instance, I want to measure the angle defined by a carbonyl vector (a vector going through a C=O bond) in my molecule and the z-axis of the simulation box. How do I define this angle, and which tool would I use to measure it in each frame of my trr? Thanks, Arneh ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Shape Yahoo! in your own image. Join our Network Research Panel today! http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] which tool to use a measure a user-defined angle in a traj
Fair enough, but I'll just repeat that g_bundle does *exactly* what you want in your example - provide it with an index file with two groups with the COMs defining the ends of the axes (in your case, one C in one group and one O in the other) and the option -z, and it'll dump out a file of the angle those axes make with the z-axis. Don't be put off by the way it appears to be designed for helices. - Original Message From: Arneh Babakhani <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Tuesday, July 17, 2007 1:30:22 AM Subject: Re: [gmx-users] which tool to use a measure a user-defined angle in a traj ok, thanks. I like Chris's suggestion. I'll try using matlab to parse it out (b/c matlab can easily ingest column formatted data), Arneh Tsjerk Wassenaar wrote: > Hi Arneh, > > I think you're out of luck here. However, this is an excellent > exercise to get started with writing custom made analysis tools :) > Alternatively, you could output the coordinates for the C and O using > g_traj and use a script to calculate the angles with the z-axis, in > case it's a single bond you're interested in. > > Cheers, > > Tsjerk > > On 7/13/07, Arneh Babakhani <[EMAIL PROTECTED]> wrote: >> Hi, >> >> Looking through the gmx tools . . . was wondering, which tool would one >> use (if such a tool exists) to measure the fluctuation of a user-defined >> angle in a trajectory. >> >> For instance, I want to measure the angle defined by a carbonyl vector >> (a vector going through a C=O bond) in my molecule and the z-axis of the >> simulation box. How do I define this angle, and which tool would I use >> to measure it in each frame of my trr? >> >> Thanks, >> >> Arneh >> >> >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Shape Yahoo! in your own image. Join our Network Research Panel today! http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] which tool to use a measure a user-defined angle in a traj
Hi Arneh, I'd sort of do the same, but would use R (http://cran.r-project.org/) :) Just a matter of taste (and of sticking to free, open-source software). Tsjerk On 7/17/07, Arneh Babakhani <[EMAIL PROTECTED]> wrote: ok, thanks. I like Chris's suggestion. I'll try using matlab to parse it out (b/c matlab can easily ingest column formatted data), Arneh Tsjerk Wassenaar wrote: > Hi Arneh, > > I think you're out of luck here. However, this is an excellent > exercise to get started with writing custom made analysis tools :) > Alternatively, you could output the coordinates for the C and O using > g_traj and use a script to calculate the angles with the z-axis, in > case it's a single bond you're interested in. > > Cheers, > > Tsjerk > > On 7/13/07, Arneh Babakhani <[EMAIL PROTECTED]> wrote: >> Hi, >> >> Looking through the gmx tools . . . was wondering, which tool would one >> use (if such a tool exists) to measure the fluctuation of a user-defined >> angle in a trajectory. >> >> For instance, I want to measure the angle defined by a carbonyl vector >> (a vector going through a C=O bond) in my molecule and the z-axis of the >> simulation box. How do I define this angle, and which tool would I use >> to measure it in each frame of my trr? >> >> Thanks, >> >> Arneh >> >> >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] which tool to use a measure a user-defined angle in a traj
ok, thanks. I like Chris's suggestion. I'll try using matlab to parse it out (b/c matlab can easily ingest column formatted data), Arneh Tsjerk Wassenaar wrote: Hi Arneh, I think you're out of luck here. However, this is an excellent exercise to get started with writing custom made analysis tools :) Alternatively, you could output the coordinates for the C and O using g_traj and use a script to calculate the angles with the z-axis, in case it's a single bond you're interested in. Cheers, Tsjerk On 7/13/07, Arneh Babakhani <[EMAIL PROTECTED]> wrote: Hi, Looking through the gmx tools . . . was wondering, which tool would one use (if such a tool exists) to measure the fluctuation of a user-defined angle in a trajectory. For instance, I want to measure the angle defined by a carbonyl vector (a vector going through a C=O bond) in my molecule and the z-axis of the simulation box. How do I define this angle, and which tool would I use to measure it in each frame of my trr? Thanks, Arneh ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] which tool to use a measure a user-defined angle in a traj
Hi Arneh, I think you're out of luck here. However, this is an excellent exercise to get started with writing custom made analysis tools :) Alternatively, you could output the coordinates for the C and O using g_traj and use a script to calculate the angles with the z-axis, in case it's a single bond you're interested in. Cheers, Tsjerk On 7/13/07, Arneh Babakhani <[EMAIL PROTECTED]> wrote: Hi, Looking through the gmx tools . . . was wondering, which tool would one use (if such a tool exists) to measure the fluctuation of a user-defined angle in a trajectory. For instance, I want to measure the angle defined by a carbonyl vector (a vector going through a C=O bond) in my molecule and the z-axis of the simulation box. How do I define this angle, and which tool would I use to measure it in each frame of my trr? Thanks, Arneh ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] which tool to use a measure a user-defined angle in a traj
Hi, I would use g_bundle with the -z option. Tom --On 14 July 2007 10:51 -0400 [EMAIL PROTECTED] wrote: For instance, I want to measure the angle defined by a carbonyl vector (a vector going through a C=O bond) in my molecule and the z-axis of the simulation box. Not sure if that tool exists. You could, however, do this: 1) use make_ndx to make an index group of only the two atoms of interest 2) trjconv -f entire.xtc -o two_atoms.gro 3) write a simple script to parse the output .gro trajectory file in order to obtain the angle to the z axis based on cos(theta)=(z2-z1)/r therefore theta=arccos[(z2-z1)/r] where the angle is defined to the negative z direction. If you used constraints for that bond then it will be especially simple, otherwise you will need good old pythagoras to get r. Note1) If you've got lots of angles that you want to average over, the process is the same but with more book-keeping. Note2) You could also try modifying template.c Good luck. PS: if you do write a script, please post it back to the list. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] which tool to use a measure a user-defined angle in a traj
For instance, I want to measure the angle defined by a carbonyl vector (a vector going through a C=O bond) in my molecule and the z-axis of the simulation box. Not sure if that tool exists. You could, however, do this: 1) use make_ndx to make an index group of only the two atoms of interest 2) trjconv -f entire.xtc -o two_atoms.gro 3) write a simple script to parse the output .gro trajectory file in order to obtain the angle to the z axis based on cos(theta)=(z2-z1)/r therefore theta=arccos[(z2-z1)/r] where the angle is defined to the negative z direction. If you used constraints for that bond then it will be especially simple, otherwise you will need good old pythagoras to get r. Note1) If you've got lots of angles that you want to average over, the process is the same but with more book-keeping. Note2) You could also try modifying template.c Good luck. PS: if you do write a script, please post it back to the list. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] which tool to use a measure a user-defined angle in a traj
Hi, Looking through the gmx tools . . . was wondering, which tool would one use (if such a tool exists) to measure the fluctuation of a user-defined angle in a trajectory. For instance, I want to measure the angle defined by a carbonyl vector (a vector going through a C=O bond) in my molecule and the z-axis of the simulation box. How do I define this angle, and which tool would I use to measure it in each frame of my trr? Thanks, Arneh ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
