Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD

From: Thomas Evangelidis <>
Date: Tue, 12 Nov 2013 19:31:20 +0200

Hi Pawel,

Thank you for the clarifications.

4. To check if your system is set up correctly one thing you can do is
convert your inpcrd file to a pdb (use ambpdb) and add a CRYST1 pdb format
record. Then in vmd you can use the periodic tab in the
Graphics->Representations window to generate periodic boundy copies of your
system: if all space is neatly tasselated, you are good.

I did that and I got exactly the same tessellation with the two images I
showed before equilibration (with gaps between boxes). This is the line I
added to the .pdb:

CRYST1 106.000 106.000 86.000 90.00 90.00 120.00 P 21 21 21 8

> 6.About your images: is that the same system? Why are there empty spaces
> there between hexagonal shaped boxes? Again, the unit cell should look like
> a triclinic cell and it is only the tasselation in space of those unit
> cells that will create a hexagonal "look". (see attached images)

Is it because I start from a hexagonal prism box generated by CHARMM-GUI?
How did you generate the triclinic box you showed? It looks like a hexagon
before wrapping (or "imaging" in AMBER language) water coordinates to the
central cell.


Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens

AMBER mailing list
Received on Tue Nov 12 2013 - 10:00:02 PST
Custom Search