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 <[email protected]> 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 list [email protected] >> 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 list [email protected] 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 list [email protected] 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
