[gmx-users] trjconv and ions

Joe Joe ilchorny at gmail.com
Thu Mar 25 19:20:22 CET 2010

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?
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