VMD-L Mailing List

From: Passerone, Daniele (Daniele.Passerone_at_empa.ch)
Date: Tue May 06 2014 - 08:25:54 CDT

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? 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.

Adding bonds between periodic images would be really great. 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.

Thank you very much for your help,

Regards,

Daniele