VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue May 06 2014 - 09:15:13 CDT

On Tue, May 6, 2014 at 9:25 AM, Passerone, Daniele <
Daniele.Passerone_at_empa.ch> wrote:

> Dear users and developers,
> I am sorry I am bringing up again a very old issue.
>
>
> I have a periodic system (polymer) and I loaded a trajectory in dcd
> format, with variable box.
> There is a bond between two carbon atoms across the boundary, in the x
> direction of a 70 angstrom box.
>
> The command
>
> topo addbond 734 752
>
> …adds a 70 angstrom long bond. There is no way to add the bond across
> the boundary. Would it be possible to add a “minimum image convention” or
> similar in the addbond routine?
>

​how should that be possible? it doesn't make any sense. if you create a
bond between those two atoms that is the bond you create. whether this bond
is interpreted between closest images of those atoms or not is a property
of the MD code you are using and has nothing to do with VMD or topotools.​
VMD by itself doesn't know anything about periodic images.

> After all, the graphical generation of the periodic images (already
> available) should use similar instructions… but I don’t know the code to
> give real advice here.
>

​that is a misinterpretation of the visuals. the periodic display in VMD is
solely done after the fact by simply replicating the principal cell
representation. no relations to periodic image are considered anywhere. the
only components in VMD that do consider periodic boundaries are a few
atomselect subcommands like "pbwithin".

> Adding bonds between periodic images would be really great.
>

​that would require new representations or extending existing
representations with a new code path. not a trivial operation​ and also
requiring considerable effort.

> The workaround of duplicating the cell ( topotools has one such function,
> but AAIK only for orthorhombic
>
cell) would be also ok, although I was not able to extend the example in
> the documentation to a whole trajectory.
>

this is best done by adding a new subcommand to topotools that extends the
replicatemol subcommand to trajectories since VMD would only be able to
store one bond topology for the entire trajectory. if the original
trajectory has been wrapped, it is not entirely straightforward to do with
without creating artefacts.

>
>
> Thank you very much for your help,
>
> Regards,
>
> Daniele
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.