Re: AMBER: periodicity problem

From: Bill Ross <>
Date: Wed, 16 Mar 2005 14:23:03 -0800 (PST)

> I'm working on an alkane chain problem in vacuo.

You apparently mean "without solvent" rather than "in vacuo."

> I set the box for periodicity with setBox vdw in leap and have
> tried various versions of periodicity during
> the equilibration but it doesn't work. What I'm seeing (vmd) are the atoms
> fixed to a certain part of the screen and then bonds becoming really
> long as the alkane chain apparantly shows up on the other side
> (it's aesthetic but not scientific),

The other way around, actually - they are translated across the
box to the correctly imaged place. You need to run a postprocess
to make them whole again, however they will then appear to stick
out of the box into space. But either way it is mathematically
correct (thus scientific :-)

ptraj has imaging for making them whole again.. see the manual
for a description.

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Received on Wed Mar 16 2005 - 22:53:00 PST
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