VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Apr 16 2013 - 04:41:53 CDT

On Tue, Apr 16, 2013 at 11:22 AM, yi <yihang2008_at_126.com> 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.

axel.

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

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

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