# Re: cellBasisVector x,y,z values

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Thu Jul 08 2004 - 10:35:11 CDT

Hi Shirley,

The values gained from the vmd measure minmax command need to be added to
give you the correct cellbasisvectors, but you also need to check the
origin of your system box to with measure center.

ie (-10 -10 -10) ( 10 10 10)

|-10| + 10 = 20
> cellBasisVector1 = 20,0,0
> cellBasisVector2 = 0,20,0
> cellBasisVector3 = 0,0,20

would be the correct syntax, however you need to check the origin to make
sure your center is really where you think it is...

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
>

*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
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