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

From: Thomas Evangelidis <>
Date: Wed, 13 Nov 2013 01:02:04 +0200

On 13 November 2013 00:06, Jason Swails <> wrote:

> On Tue, Nov 12, 2013 at 4:11 PM, Thomas Evangelidis <
> >wrote:
> > One more detail. When I use in NAMD :
> >
> > wrapWater on
> > wrapAll on
> > wrapNearest off
> >
> > I get the hexagonal prism I showed, but when I set:
> >
> I presume you mean "wrapNearest on" here, right?


> >
> > wrapWater on
> > wrapAll on
> > wrapNearest off
> >
> > I get exactly the triclinic box you showed.
> >
> 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.
I got it now. Many thanks Jason for the detailed explanation.

Should I worry about the gaps between the hexagonal shaped boxes in the
initial configuration of the periodic system? These gaps are filled up
once the equilibration progresses and the system assumes the shape of the
unit cell described by the last line of .inpcrd and NAMD parameters
cellBasisVector1, cellBasisVector2, cellBasisVector3. If these parameters
were defined correctly would the gaps at the beginning pose a problem?

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

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Received on Tue Nov 12 2013 - 15:30:02 PST
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