From: Marek Maly (
Date: Fri Apr 16 2010 - 09:59:50 CDT

Dear all,

I am trying to visualize my molecular system which was calculated
using cubic periodic box.

Here you can find relevant PSF/PDB file along with my visualization
script which I run through VMD Tk extension.

The PDB was saved during the calculation in unwraped coordinates (to show
all original molecules without PBC effects).

I would like to have system visualised inside the periodic box but of
without visualizing bonds which arrise from the different parts of one
which was splitted due to periodic conditions.

I tried experimented with recommended combination of commands:

pbc wrap
pbc join
pbc unwrap

(please see the commented lines in my script "vmd_anim.tcl" ) but this
didn't help me much :((

I probably didn't understand well this approach so I forget maybe some
parameters and so on ...

Is there anyone able to correct my "vmd_anim.tcl" so that the system is
visualized in simulation
box in resonable way it means:

That the molecules which are broken due to the PBC are visualised in
complete shape
however with some part of the molecule outside the simul. box. If the given
molecule is splitted in several pieces by PBC, the position of the
complete molecule
could be chosen due to the position of the biggest fraction.

If a) is problem, I would like to know how to "disable" (of course by
script command if possible)
unwanted bonds over whole simul. box. which connect splitted parts of one

Thank you very much for any useful ideas !

Best wishes,


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