Periodic Boundary Condition in NAMD

From: Van Ngo (nvan_at_usc.edu)
Date: Thu Jun 02 2011 - 23:55:08 CDT

Dear NAMD users,
I am trying to understand how Periodic Boundary Condition (PBC) works
in NAMD code.
Is it true that when we turn on WrapAll option, PBC is applied every step?
Since the output coordinates will be wrapped around PBC box for a
certain frequency (multiple of steps), so does it mean that these
coordinates are the same as the coordinates being run by the code? Or
is there any difference between the output coordinates and the
coordinates being processed in NAMD?

I have looked in the code, but could not find where PBC is explicitly
applied to wrap particles back to the PBC cell every step.

Any suggestions will be very appreciated.

Best,
Van

-- 
Van Anh Ngo
Graduate Student
Department of Physics & Astronomy
University of Southern California
Los Angeles, CA 90089-0242

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