VMD-L Mailing List

From: Kevin Wittkowski (kevin.wittkowski_at_epfl.ch)
Date: Fri Jun 14 2024 - 02:43:55 CDT

Dear Giacomo,

thanks for your kind reply.

If I use topo addbond as you suggest, what should I use as a source and destination for the bond?

Let's imagine I have a simple structure of 9 atoms in a square grid like this

1_2_3

4_5_6

7_8_9

Would you do

topo addbond 1 7

topo addbond 2 8

topo addbond 3 9

topo adddbon 1 3

topo addbond 4 6

topo addbond 7 9

or is there a way to specify that we want the periodic image of each atom to be taken? for example, the structure with a periodic image would be

1_2_3 1'_2'_3'

4_5_6 4'_5'_6'

7_8_9 7'_8'_9'

and the command (abusing a bit the notation)

topo addbond 3 1'

topo addbond 6 4'

..

Thanks in advance for your help.

Best,

Kevin Wittkowski

Assistant-Doctorant

EPFL STI LFMI

ME D2 2715

1015 Lausanne

________________________________
Da: giacomo.fiorin_at_gmail.com <giacomo.fiorin_at_gmail.com>
Inviato: giovedì 13 giugno 2024 23:37:32
A: Kevin Wittkowski
Cc: vmd-l_at_ks.uiuc.edu
Oggetto: Re: vmd-l: bonding across periodic walls

Hi Kevin, I have personally used in a paper<https://urldefense.com/v3/__https://doi.org/10.1080/00268976.2021.1948122__;!!DZ3fjg!6EOV0mHcW2gxm8LMsTt4mz8xVDQNbzgvc1q5JdPG7adNF3PG2Nu5nTlRIvv-bIyFxqpqMfKF7-Jp0IWFRmnzeO3G2noSdQ$ > 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<mailto: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