Re: [AMBER] how to calculate electron density and order parameters of lipid11 membrane

From: Jason Swails <>
Date: Tue, 19 Nov 2013 20:16:01 -0500

On Tue, Nov 19, 2013 at 4:43 PM, Thomas Evangelidis <>wrote:

> I found the reason for underestimating the electron density. When I wrapped
> the hexagonal cell to an orthorhombic box, hid the waters and displayed the
> periodic cells along the x and y axes, I saw there were gaps.

A hexagonal cell and a truncated octahedron are different box shapes, so
you can't image one into the other. You could fit one inside the other
(assuming the other was large enough to circumscribe it), but then you'll
obviously have gaps. It would be like fitting a sphere inside a cube and
tiling the cube -- there will be a lot of 'gaps'.

> In contrast,
> when I wrapped to a parallelepiped box there were no gaps. However, the
> Density Profile VMD plugin works only with orthorhombic boxes. Is it
> possible to convert my hexagon to an orthorhombic box with "image"
> directive of cpptraj?

No. They are fundamentally different box shapes (they have different space
group symmetry). It's effectively the same thing as when you tried mapping
the hexagonal cell into a truncated octahedron.

I'm not familiar with the density profile plugin, but VMD does recognize
arbitrary triclinic cells, I'm pretty sure. You may have to set them using
the TCL interface; I've never really looked into this in much detail.
 There's no guarantee it would work with the Density Profile plugin if it
was coded specifically to handle only orthorhombic boxes.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Nov 19 2013 - 17:30:04 PST
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