[gmx-users] Pulling: Fix the position of a molecule

[Daniele Veclani]

Dear Gromacs Users

I'm simulating a system of two molecule (A,B unbound). Right now, I am trying
to generate the configurations and then make Umbrella Sampling Simulations.

I have this problem: While I generate the configurations I observed that the
molecule A comes out of the box and makes the calculation fail.

I've used the position restraint generating posre.itp file for molecule A, but
analyzing the trajectories I see that the molecule A moves and comes out of
the box.

How can I fix the problem? I attached my files for the topology, and
poste.itp .mdp

I use Gromacs 5.0.4.

Best regards.
D.V.