From: Neelanjana Sengupta (
Date: Sun May 11 2008 - 02:04:57 CDT

Dear VMD users,

Can anybody ascertain if the 'within' command takes into account periodic
boundary conditions? In other words, for obtaining the atoms 'within' a
certain distance of a selection, is the distance between the selection and
each atom recalculated as:
dx=dx - cell_a*NINT(dx/cell_a), etc?

This is for a dcd file where the unit cell dimensions are specified at each

Neelanjana Sengupta