Thanks, that makes sense. On Thu, Mar 25, 2010 at 12:15 PM, Tsjerk Wassenaar <[email protected]>wrote:
> 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 >
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