VMD-L Mailing List

From: Olaf Lenz (lenzo_at_mpip-mainz.mpg.de)
Date: Wed Aug 12 2009 - 09:06:01 CDT

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Florentina Tofoleanu wrote:
> I have a question about how VMD "sees" periodic cells. I use periodic
> boundaries in my simulations, so when running the resulting .dcd file in
> VMD, the molecules that go over the top of my simulation box, I see them
> at the bottom of the box(and have negative z coodrinates). When getting
> the RMSD for the whole molecular system I get these jumps whenever that
> happens.

Note, BTW, that it is not VMD that changes the coordinates, but the
simulation program. VMD only shows exactly what is in the DCD-file. So
if there are jumps in the coordinates, they come from the simulation.
However, the VMD pbctools provide means to modify the coordinates such,
that they are easier to visualize. And one of this is that it allows to
"unwrap" trajectories, i.e. it removes the jumps that occur when the
coordinates are wrapped about the periodic boundaries.

Olaf

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