Periodic boundary conditions and replicating cells

(under construction)

bonds across the cell?

got to Graphics, Representation a new window will open

select the current representation and change the Drawing Method from lines to Dynamic Bonds

Graphical presentations -> Periodic

you have to select all for the representation as only the representation highlighted is replicated

note that this does not really work all that well!
link to the online instructions from vmd http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
how to use the PBC plugin

first load the trajectory file and wait for it to finish loading

use the following pbc command

to see if the data has already been read in, this can be the case with dlpoly HISTORY files

pbc get

if the pbc are not there then you need to set the a b c cell size (angstrom) vectors via command line (here I've used 42)

pbc set { 42 42 42} –all

wrap coordinates around origin

pbc wrap –center origin –all

get all bonds back to normal

pbc join res –border 3 –all

-all means apply to all frames of the trajectory