AW: wrapping in two dimensions

From: Norman Geist (
Date: Fri Oct 17 2014 - 02:21:07 CDT

Why not simply have a look at the „periodic” tab for representations? ;)

Create a representation for the membrane only and show its periodic Z image. So you can see both interacting sites at a time.


BTW this is a vmd question, isn’t it !?


Norman Geist.


Von: [] Im Auftrag von Maria Bykhovskaia
Gesendet: Donnerstag, 16. Oktober 2014 22:34
Betreff: namd-l: wrapping in two dimensions



Is it possible to wrap around a part of the system in one or two dimensions?

Here is the problem:

I model a protein on the top of the lipid bilayer. I have periodic conditions with flexible cell. The membrane stays in place, the protein moves around. At some frames it moves laterally, and part of the protein shifts out of the cell. However, I can see that the protein actually should interact with the mirror image of the membrane, since it is on the same level with the membrane at Z ax (the membrane is on XY plane). I want to visualize the interaction of the protein with the membrane continuation (mirror image).

I have aligned and recentered the system around the protein. When I wrap around the whole thing, the membrane image is on the top of the protein, and that does not help.

Is there any way I can wrap the membrane laterally, over XY (or just over X) without changing its Z position?

Will greatly appreciate any ideas.





Maria Bykhovskaia
Professor and Chair, Neuroscience Department
Director, Specialized Neuroscience Research Program
Universidad Central del Caribe
Bayamon, Puerto Rico
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