From: Axel Kohlmeyer (
Date: Tue Apr 16 2013 - 04:41:53 CDT

On Tue, Apr 16, 2013 at 11:22 AM, yi <> wrote:

> Dear VMD users,****
> I encountered a problem of handling periodic boundary conditions
> when displaying h-bond between water molecules. For example, I used
> Graphics-Representations-Periodic( along Y direction), but there is no
> h-bond displayed at the edge of periodic box. The h-bond between water
> molecules in the box displayed well. The following is one of my
> problematic image. Is there any method to show h-bond between original
> image and periodic image? Thank you in advance.

the periodic display in VMD is just replicating the visualization of a
single cell *after* it has been computed. to get a real periodic display,
you have to replicate the trajectory data.


> ****
> Best regards.****

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