Re: Hexagonal boundary conditions

From: Alessandro Cembran (
Date: Thu Sep 21 2006 - 10:34:51 CDT

Hi Harindar,

Sorry for not having noticed your post earlier. In order to get an
hexagonal patch, you need to use "WrapNearest on".
The vectors I use are the following:
v1 = ( r ; 0 ; 0 )
v2 = ( r/2 ; sqrt(3)*r/2 ; 0 )
v3 = ( 0 ; 0 ; h )
With r being the inner radius of the hexagon and h the height of your box.
The Hexagonal patch has to be oriented in such a way that it's centered
in the origin and with two sides perpendicular to the X-axis.


Harindar Keer wrote:
> Dear All,
> I started with hexagonal patch of membrane, on minimizing the
> system, it takes the shape of parallelogram. I was wondering if this
> is the way NAMD takes care of hexagonal BCs. For cell basis vectors, I
> am using non-orthogonal vectors. It would be great if any one can
> confirm it or suggests how hexagonal BCs should be setup.
> Thanks,
> Harindar

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