[gmx-users] Box Borders

ifat shub shubifat at gmail.com
Wed Jul 4 10:17:24 CEST 2012

I am running a simulation of a protein-protein complex using explicit
solvent. (mdrun -v -deffnm run)
I created a box for the simulation (d=5) using editconf:
editconf -princ -f conf.gro -bt dodecahedron -d 5.0 -c -o box.gro
I am using the option pbc=no in the run.mdp file.
Can anyone explain what happens if the complex reaches the "walls" of
the box? Does the complex return to the box with the enrgy gained from
the collision? Can the complex cross the "walls"?

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