# Re: cellBasisVector x,y,z values

From: Edward Patrick Obrien (edobrien_at_Glue.umd.edu)
Date: Thu Jul 08 2004 - 09:36:43 CDT

Hi Shirley,

I don't think your interpretation is correct.
This is what they are:
cellBasisVector1 = |min(x)-max(x)|,0,0
cellBasisVector2 = 0,|min(y)-max(y)|,0
cellBasisVector3 = 0,0,|min(z)-max(z)|

The cell basis is just the length of the side of the cube, cell origin
defines where the cube is located.

Ed

On Thu, 8 Jul 2004, Shirley Hui wrote:

> I was wondering if someone could confirm if my understanding is right.
>
> When setting the cellBasisVector1, cellBasisVector2, cellBasisVector3 for
> Periodic Boundary conditions in the NAMD config file:
>
> cellBasisVector1 = x,0,0
> cellBasisVector2 = 0,y,0
> cellBasisVector3 = 0,0,z
>
> The x,y,z are the minimum OR maximum values obtained by running the command
> in VMD:
>
> > set everyone [atomselect top all]
> > measure minmax \$everyone
>
> Can someone please confirm if this is correct?
>
> The tutorial Statistical Mechanics of Proteins doesn't explicitly indicate
> that the x,y,z values should be min or max - infact it doesn't tell you how
> to obtain the x,y,z values.
>
> The tutorial infact says:
>
> "Three periodic cell basis vectors are to be specified to give the periodic
> cell its shape and size. They are cellBasisVector1 , cellBasisVector2, and
> cellBasisVector3 . In this file, each vector is perpendicular to the other
> two, as indicated by a single x, y, or z value being specified by each. For
> instance, cellBasisVector1 is x = 42Å, y = 0Å, z = 0Å. With each vector
> perpendicular, a rectangular 3-D box is formed."
>
> http://www.ks.uiuc.edu/Training/SumSchool/materials/sources/tutorials/02-namd-tutorial/namd-tutorial-html/node9.html#SECTION00025100000000000000
>
> Where they came up with the value for x,y,z is not explicitly indicated.
> But if my understanding is correct I believe it should be the min max
> values.
>
> Thanks,
> shirley
>

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