Re: about interaction between protein and its image in namd simulation

From: Aron Broom (
Date: Tue Jul 09 2013 - 13:10:50 CDT


To be safe, you should either use a square box (or something else with all
axes equal) or restrain rotation of the protein to keep the longest protein
axis aligned with the longest box axis. I think there is a tutorial or a
page in the user guide that shows an example of this kind of restraint.


On Tue, Jul 9, 2013 at 1:16 PM, Liqun Zhang <> wrote:

> Dear namd users:
> I set up a rectangular box to solvate a protein complex (dimer) using
> water molecules. The size of the box is like following: 90 A, 80 A, and 70
> A. The cutoff is around 12 A. Since the complex can do random global
> movements inside the box, can the rectangular box cause any extra
> interaction between the protein and its image once the longest axis of the
> complex aligned to the shorted side? Thank you very much.
> Best regards,
> Lqz

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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