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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