[gmx-users] pbc problem

[shahab shariati]

Dear Tsjerk Wassenaar

Very very thanks for your reply.

I used trjconv -pbc mol.

pbc problem was solved only for lipid molecules.

When I see new trajectory by vmd, there are some problesm about drug
molecule.

https://www.dropbox.com/s/xq4s6az17buhvb8/images-2.docx

If I show my system as 4 regions, my system before equilibration is as
fallows:

region (1): water + drug
region (2): top leaflet of bilayer
region (3): bottom leaflet of bilayer
region (4): water

After equilibration, drug molecule exits region (1) and enters region (4),
alternately.

On the other hand, drug molecule is in region (1)in some frames and is
in region (4) in other frames.

Please tell me how to fix it? Is this issue (about drug molecule) pbc
problem?

Best wishes