[gmx-users] pbc problem

shahab shariati shahab.shariati at gmail.com
Thu Oct 24 16:57:45 CEST 2013

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

More information about the gromacs.org_gmx-users mailing list