Re: Periodic Boundary Condition in NAMD

From: Jim Phillips (
Date: Fri Jun 03 2011 - 09:57:38 CDT

Wrapping is done internally when atoms are assigned to or migrate between
patches on cycle boundaries. On output these transformations are first
undone and then wrapWater/wrapAll are applied before writing to the file.


On Thu, 2 Jun 2011, Van Ngo wrote:

> 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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