[gmx-users] pbc problem

[shahab shariati]

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
true.

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

https://www.dropbox.com/s/d0hppxdngj7xwst/em2.gro

https://www.dropbox.com/s/gnqf6fuxwwj0zzt/npt.gro

https://www.dropbox.com/s/w899y86mhp0ysbo/0.xtc

Best wishes