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

From: Daniel Roe <>
Date: Tue, 12 Nov 2013 15:27:32 -0700

On Tuesday, November 12, 2013, Jason Swails wrote:
> I had a conversation with Pawel about this and it's because these two
> representations are equivalent. A hexagonal prism replicated periodically
> can be represented as a simple triclinic cell with certain angles between
> the unit cells (90, 90, and 120 degrees, for instance). Imagine cutting
> off corners and attaching them to the opposite side in such a way that
> every particle is represented with the periodic image closest to a
> particular point in space. The imaging routines are generalized for
> triclinic cells, so by default they will give you the triclinic cell Pawel
> showed. If you instead take the image that is closest to a particular
> point in space, then you will (necessarily) get the most spherically
> symmetrical representation of that triclinic cell, which in your case is a
> hexagonal prism.
> This is the difference between using and not using the "familiar" keyword
> in the (cp)ptraj image commands, I believe.
> This is correct, and also why 'image familiar' is a bit slower.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
AMBER mailing list
Received on Tue Nov 12 2013 - 14:30:04 PST
Custom Search