[gmx-users] pbc problem

shahab shariati shahab.shariati at gmail.com
Sun Oct 27 13:16:46 CET 2013

Dear Justin

I want to study translocation of drug molecule in lipid bilayer.

My gro file after minimization is em2.gro.

After NPT-MD simulation, I obtained npt.gro and 0.xtc files.

When I see trajectory by vmd, there are some things abnormal.

I guess there is pbc problem.

I attached these 3 files. Please after viewing them, tell me is my guess

If yes, please guide me how to fix it. If no, please tell me what is




Best wishes

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