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.
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