Re: How does NAMD treat a bond across periodic boundaries

From: Axel Kohlmeyer (
Date: Thu Jul 12 2012 - 01:56:00 CDT

On Thu, Jul 12, 2012 at 6:17 AM, <> wrote:
> Hi Everyone
> 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).
> H
> |
> ---------|----------- -> periodic boundary
> |
> H
> 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.

you NAMD uses the "nearest neighbor coordinates".
no problem. have a look at one of the many MD textbooks
that explain basic MD principles including PBC.


> Thank you in advance.

> Regards
> M.J. Aghaei

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

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