VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Jun 13 2024 - 16:37:32 CDT

Hi Kevin, I have personally used in a paper
<https://urldefense.com/v3/__https://doi.org/10.1080/00268976.2021.1948122__;!!DZ3fjg!7lsEx5h6koxFcM577dqO1uXVk03w_WvcJayELXIMu_USrU4dZ2ozl6MT8e8IX2KlM1PrkAoOMpIUH3TDZcDD6VV6sg$ > the "topo addbond" command
to create bonds that straddle a periodic boundary:
https://www.ks.uiuc.edu/Research/vmd/plugins/topotools/#TOC-addbond-id1-id2-

VMD may not visualize them in the clearest way, but they ran fine for
simulation.

Giacomo

On Thu, Jun 13, 2024 at 5:34 PM Kevin Wittkowski <kevin.wittkowski_at_epfl.ch>
wrote:

> Dear Sir, Madam
>
> using VMD with the graphene and nanotube tcl commands and using TopoTools
> and the .inp file attached, I created the structure you find in attachments.
>
> It is constituted of 4 graphene layers and a carbon nanotube.
>
> By inspection in VMD, the bonds created internally are correct, however, I
> would like to create also the bonds that wrap around the periodic box.
>
>
> How can I perform this operation?
>
>
> Thanks beforehand.
>
> Best regards,
>
>
> *Kevin Wittkowski*
>
> *Assistant-Doctorant *
>
> EPFL STI LFMI
>
> ME D2 2715
>
> 1015 Lausanne
>
>