VMD-L Mailing List

From: Diego Gomes (diego.enry_at_gmail.com)
Date: Mon Nov 20 2023 - 22:34:43 CST

Hi Patrick,
to complement Jason's message.

Graphics -> Representations -> Periodic
Picking +X, -X, +Y, -Y should do the trick.

Friendly,
Diego.

On Thu, Nov 16, 2023 at 4:07 PM Jason Smith <jason_smith_18_at_sfu.ca> wrote:

> What about rendering multiple boxes but only having the molecules of
> interest visible?
>
>
>
> Cheers,
> -
> Jason Smith
> Post-Doctoral Fellow
> Robert N. Young Lab, Simon Fraser University
> 8888 University Drive, Burnaby, BC, V5A-1S6
> Canada
>
> ------------------------------
> *From:* owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of
> Patrick Charchar <patrick.charchar_at_rmit.edu.au>
> *Sent:* Wednesday, 15 November 2023 9:27:39 PM
> *To:* vmd-l_at_ks.uiuc.edu
> *Subject:* vmd-l: Smoothing PBC jumps across PBC
>
>
> RMIT Classification: Trusted
>
> Hi all,
>
>
>
> I’m visualising a membrane simulation and was wondering if there is a way
> to smooth the distracting jumps as lipids move across the PBC?
>
>
>
> To be clear, I’m not talking about wrapping – my molecules are whole (no
> visual bonds break). I simply want to slow down the distracting visual
> effect at the box edges of having molecules constantly appearing and
> disappearing as they move from one side of the cell to another.
>
>
>
> Thanks in advance,
>
> Patrick
>
>
> 

-- 
Diego Enry B. Gomes, PhD
Department of Physics at Auburn University &
NIH Center for Macromolecular Modeling and Visualization
Leach Science Center - Ste. 3182 - Auburn, AL
dgomes_at_auburn.edu