Re: [Periodic Boundary]: from charmm to namd

From: Charles Danko (
Date: Tue Nov 02 2004 - 11:35:23 CST


As I understand it, you should be able to use a different cell
geometry with the "wrapAll on" parameter for your purposes.


On Tue, 02 Nov 2004 16:08:42 +0100, Sascha Tayefeh
<> wrote:
> Dear Community,
> I have continuously encountered the same problem with many systems
> created with charmm, and this is:
> Supposing, I have used an orthorombic cell in charmm for periodic
> boundary (pb), I would have to use significantly higher values for cell
> dimensions in order to make this system run with namd. However,
> initially working with a canonic ensemble, I may not change
> cell-dimensions during namd-run.
> I have realized, that the order, of which the dimensions need to be
> increased are the same as the atoms of the molecules that were not
> wrapped, anyway, if so, why does namd not (or falsely?) realize wrapped
> atoms? Or better:
> How can I use same cell dimensions in namd I used in charmm?
> Sincerely
> --
> Sascha T.

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