[gmx-users] trjconv and ions

[Joe Joe]

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?
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100325/ab1c18b4/attachment.html>