VMD-L Mailing List

From: MD Simulation (mdsimulationgroup_at_gmail.com)
Date: Sat Nov 27 2021 - 07:46:25 CST

Thanks Axel, that's what I suspected so thanks for confirming.

On Sat, Nov 27, 2021, 8:45 AM Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> Periodic display in VMD is done by replicating the visualization from the
> principal cell.
> Because of that, no bonds across periodic boundaries can be visualized.
> If you want to see those, you will have to create a custom trajectory file
> with the desired replicated positions and then visualize that.
>
> On Sat, Nov 27, 2021 at 8:36 AM MD Simulation <mdsimulationgroup_at_gmail.com>
> wrote:
>
>> Hello,
>>
>> I'm running a reactive MD and would like to visualize the bonds using
>> dynamic bonds but bonds are not handled across PBC. Are there any
>> suggestions on dealing with bond formation across PBC?
>>
>> Thanks,
>> Joe
>>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!tVqNwrsraqVmeBo-rlMOgv93JQjiiojOFblX7mfFWvI7mzmQxMew2ndf-hyyeiKQnw$
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>