[gmx-users] trjconv and ions

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Mar 25 20:15:40 CET 2010

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,


On Mar 25, 2010 7:22 PM, "Joe Joe" <ilchorny at gmail.com> 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?

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