Re: [gmx-users] positions and velocities of COM of whole water molecules instead of those of individual atoms?
Dear GROMACS Masters, is there a trick to obtain coordinates and velocities of center of mass of each water molecule? Have a look at g_traj, although to analyze each molecule separately could take many iterations with specific index groups. g_traj can really do it (for coordinates), thanks! g_traj with -mol option was what I needed. It is documented in the third sentence of the DESCRIPTION section of g_traj manual... When -mol is set, the numbers in the index file are interpreted as molecule numbers and the same procedure as with -com is used for each molecule. -Bohumir ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] positions and velocities of COM of whole water molecules instead of those of individual atoms?
Dear GROMACS Masters, is there a trick to obtain coordinates and velocities of center of mass of each water molecule? Currently, the positions and velocities of *each individual atom* of all water molecules are written to the traj.trr file. I would like to look at velocity profiles, but not those of individual water atoms - rather of the whole water molecules. Maybe new xdrfile-1.0.tar.gz library can help to convert traj.trr file to have molecular COM coordinates and velocities? Thanks for a great tool, -Bohumir ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] positions and velocities of COM of whole water molecules instead of those of individual atoms?
Quoting bohumir bohu...@gmail.com: Dear GROMACS Masters, is there a trick to obtain coordinates and velocities of center of mass of each water molecule? Currently, the positions and velocities of *each individual atom* of all water molecules are written to the traj.trr file. I would like to look at velocity profiles, but not those of individual water atoms - rather of the whole water molecules. Maybe new xdrfile-1.0.tar.gz library can help to convert traj.trr file to have molecular COM coordinates and velocities? That, or you can use the GROMACS libraries to do the analysis. If you don't publish your code then it may have any license whatever; if you publish it then it (as GROMACS) must be licensed under GPL. If there isn't a tool as such already available, it should be trivial to code. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] positions and velocities of COM of whole water molecules instead of those of individual atoms?
bohumir wrote: Dear GROMACS Masters, is there a trick to obtain coordinates and velocities of center of mass of each water molecule? Have a look at g_traj, although to analyze each molecule separately could take many iterations with specific index groups. -Justin Currently, the positions and velocities of *each individual atom* of all water molecules are written to the traj.trr file. I would like to look at velocity profiles, but not those of individual water atoms - rather of the whole water molecules. Maybe new xdrfile-1.0.tar.gz library can help to convert traj.trr file to have molecular COM coordinates and velocities? Thanks for a great tool, -Bohumir ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
