From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jul 12 2012 - 01:56:00 CDT
On Thu, Jul 12, 2012 at 6:17 AM, <mj_aghaei_at_aut.ac.ir> 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.
cheers,
axel.
> Thank you in advance.
>
> Regards
> M.J. Aghaei
> mj_aghaei_at_aut.ac.ir
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy.
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