[gmx-users] are there LJ interactions from periodic images in the z directions with pbc=xyz and ewald_geometry=3dc?
Dear GROMACS Masters, when I specify pbc=xyz ewald_geometry=3dc then I believe that the PME slab correction is applied according to Y. In-Chul and M. L. Berkowitz, J. Chem. Phys. 111 (1999) pp. 3155-3162. But I would think there are still LJ interactions from periodic images in the z direction, are there? Thanks, -Bohumir -- 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] 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
