Article ID: 1630 - Last Modified: November 17, 2011
The solute is outside the simulation box. What is wrong with my Desmond simulation?
There is nothing wrong with your Desmond simulation. As as result of the periodic boundary conditions used in molecular dynamics (MD) simulations, atoms move out of the box and reappear on the opposite side. For ease of visualization, Desmond only wraps the atoms when the entire solute has moved outside the box (otherwise, at times, the solute would appear split across the box). However, this is for visualization purposes only, and the physics of the simulation are completely unaffected.
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