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

[Morteza Chehelamirani]

Thanks Jacek for your reply.

Yes, I do use VMD to vidualize the trajectory. My problem is that the
trajectory is written in an xyz format and doesn't have the cell
information in it. I'm wondering what keywords in DFTB+ I need to set to
save the cell information in an MD simulation?

Morteza Chehel Amirani, PhD
Svante, BC, Canada


On Fri, Jul 14, 2023 at 1:23 PM Jacek Jakowski <jjakowski at gmail.com> wrote:

> 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
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