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

[Jacek Jakowski]

... and that is exactly the case i gave you the prescription for.  All you
need is to enter the PBC info.
The only problem would be if your lattice constant were changing  with very
frame, but even then it  wouldn't likely matter as the changes are probaly
small and potential distortion on the picture are small.
Jacek



On Fri, Jul 14, 2023, 5:10 PM Morteza Chehelamirani <
morteza.amirani at gmail.com> wrote:

> 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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