[gmx-users] pbc problem

[shahab shariati]

Dear Mark

Thank for your reply.

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).

Please tell me how to fix it? Which options of trjconv are appropriate
for this problem?

Best wishes