Re: [gmx-users] get 3 roation angles over time
You could use g_principal and follow the change in angles of the three principal axes of your group using simple maths. This might give you what you are looking for. Another way to look at rotations is to use the program DynDom, but this only works on individual structures not trajectories. Tom --On Friday, January 01, 2010 10:49:44 +0100 Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Marc, Which rotation angles? I suppose you mean the Euler angles, but then, XYZ, XYX, ZYZ? I may be able to help. Contact me off list if you're interested. Cheers, Tsjerk On Fri, Jan 1, 2010 at 9:02 AM, marc.spen...@gmx.net wrote: Dear Gromacs users, my system consists of two rigid bodies a and b. The body a has no rotation or translation over time. Body b rotates and translates over time. For my system I got the initial structure as PDB file and a XTC trajectory. How do I get in any easy way from the XTC trajectory the three rotation angles of the rigid body b over time (someting like a 3 column output file) ? I already searched the gromacs mailinglist and I locked at the commands g_rms, g_rdf, g_sorient, g_chi, g_confrms, g_bundle and g_rmsf. But it seems that non of the commands really does what I want :( . Any help is welcome, thanks and a happy new year Marc -- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01 -- gmx-users mailing list gmx-us...@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] get 3 roation angles over time
Dear Gromacs users, my system consists of two rigid bodies a and b. The body a has no rotation or translation over time. Body b rotates and translates over time. For my system I got the initial structure as PDB file and a XTC trajectory. How do I get in any easy way from the XTC trajectory the three rotation angles of the rigid body b over time (someting like a 3 column output file) ? I already searched the gromacs mailinglist and I locked at the commands g_rms, g_rdf, g_sorient, g_chi, g_confrms, g_bundle and g_rmsf. But it seems that non of the commands really does what I want :( . Any help is welcome, thanks and a happy new year Marc -- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] get 3 roation angles over time
Hi Marc, Which rotation angles? I suppose you mean the Euler angles, but then, XYZ, XYX, ZYZ? I may be able to help. Contact me off list if you're interested. Cheers, Tsjerk On Fri, Jan 1, 2010 at 9:02 AM, marc.spen...@gmx.net wrote: Dear Gromacs users, my system consists of two rigid bodies a and b. The body a has no rotation or translation over time. Body b rotates and translates over time. For my system I got the initial structure as PDB file and a XTC trajectory. How do I get in any easy way from the XTC trajectory the three rotation angles of the rigid body b over time (someting like a 3 column output file) ? I already searched the gromacs mailinglist and I locked at the commands g_rms, g_rdf, g_sorient, g_chi, g_confrms, g_bundle and g_rmsf. But it seems that non of the commands really does what I want :( . Any help is welcome, thanks and a happy new year Marc -- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01 -- gmx-users mailing list gmx-us...@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
