Hi Joe, Probably you have a mismatch between your reference structure and the trajectory. So trjconv assumes coordinates associated with ions, while they actually belong to water.
Hope it helps, Tsjerk On Mar 25, 2010 7:22 PM, "Joe Joe" <[email protected]> wrote: I am seeing weird behavior when I trjconv my trajectory containing NaCl, tip3p, and protein. I use the OPLSAA force field and octahedral PBCs. When I run trjconv -f traj.trr -s topol.tpr -pbc nojump -o trajout.xtc The ions in the output form clusters of three similarly charged ions in the shaped like a triangle. If I look at the non trjconved trajectory everything looks fine. Any thoughts? -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
