On 4/07/2012 6:17 PM, ifat shub wrote:
Hello,
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?
The simulation system is always of infinite extent. You chose for it to
be non-periodic. There are no walls in either case.
Mark
Does the complex return to the box with the enrgy gained from
the collision? Can the complex cross the "walls"?
Thanks,
Ifat
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