VMD-L Mailing List

From: Olaf Lenz (lenzo_at_mpip-mainz.mpg.de)
Date: Wed Aug 12 2009 - 08:43:09 CDT

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Hi!

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.

What you describe sounds like a job for "pbc unwrap", which will try to
remove all jumps happening between adjacent frames. Just try to execute
"pbc unwrap" in the VMD console.

Olaf
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