[DFTB-Plus-User] trajectory file in MD for periodic models

[Jacek Jakowski]

Hi,

 you don't do this  in  DFTB, but in the VMD terminal. Here are my notes
(example for   orthorhombic lattice  14.3x14.3x14x Angstrom^3):

Go to "VMD main" menu -->  "Extensions" --> "Tk Console"  then type:

(DFTB) 19 %

(DFTB) 19 % pbc set {14.3 14.3 14.3} -all     # Set lattice  here in
angstrooms

(DFTB) 20 %

(DFTB) 20 % pbc box -center origin              # If box is weirdly
centered then try instead this:

(DFTB) 21 %                                                    # pbc box

Then to draw multiple images go to "Graphical representation" menu   and
select "periodic" from "Draw style/ Selections/ Trajectory/ Periodic" and
choose how many periodic images you want to draw.

You can also type   pbc help  to see available options.

Here is the link with more info:
https://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/



Jacek

On Fri, Jul 14, 2023 at 12:30 PM Morteza Chehelamirani <
morteza.amirani at gmail.com> wrote:

> Hello
>
> Just wondering how the trajectory file of a dynamic simulation can be
> written including the unit cell information so I can visualize the
> trajectory of the whole unit cell in VMD? For the periodic models, I see
> the trajectory written in xyz format but I need to also have cell vectors
> and angles in each step so I can better visualize.
>
> Sincerely,
> Morteza Chehel Amirani, PhD
> Svante, BC, Canada
> _______________________________________________
> DFTB-Plus-User mailing list
> DFTB-Plus-User at mailman.zfn.uni-bremen.de
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.zfn.uni-bremen.de/pipermail/dftb-plus-user/attachments/20230714/f4587cb4/attachment.htm>