VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 21 2018 - 10:32:18 CDT

Hi,
  Not presently, but this is something that could be addressed
with some revisions to the math for computing nearest neighbors.
There would be performance loss across the board, and some minor
gotchas with under-specified PBC cells with some file formats and
some fancy non-rhombic cell shapes we wouldn't get right, but if
support for these cases were added with a user-selected checkbox,
that would at least mean that users could disable it if it were
either too slow or not working as expected. This is something
that is on my TODO list after I get past some issues with
QM/MM visualization features that also need changes/updates.

Best,
  John

On Wed, Mar 21, 2018 at 11:44:55AM +0100, sperez14_at_us.es wrote:
> Dear VMD comunity,
>
> I am trying to use a polyhedra representation and also show additional
> periodic images. In the border between the images there are no polyhedra
> so I guess the NNeighbour algorithm does not look in other images. Is
> there a way to get around this? I imagine the same is true for dynamic
> bonds and such.
>
> Thank you for your help!
>
> Regards,
>
> Sergio 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/