Date: Wed Jul 11 2012 - 23:17:49 CDT
I have a question in mind about the fundamentals of NAMD. Suppose that a hydrogen gas molecule reaches a periodic boundary in a way that one of its atoms crosses the boundary and the other does not cross (schematic below).
---------|----------- -> periodic boundary
As far as I know about the periodic boundary condition, the coordinates for the atom that has exited the boundary are updated such that that atom enters the periodic cell from the opposite side. The question is that how NAMD calculates the bonded parameters, with one of the bonded atoms at one side of the cell and another one at the other side.
Thank you in advance.
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