**From:** Edward Patrick Obrien (*edobrien_at_Glue.umd.edu*)

**Date:** Thu Jul 08 2004 - 09:36:43 CDT

**Next message:**Kamp, Marc vander: "RE: cellBasisVector x,y,z values"**Previous message:**Shirley Hui: "Warning: Not all atoms have unique coordinates."**In reply to:**Shirley Hui: "cellBasisVector x,y,z values"**Next in thread:**p.w.fowler_at_qmul.ac.uk: "Re: cellBasisVector x,y,z values"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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

**Next message:**Kamp, Marc vander: "RE: cellBasisVector x,y,z values"**Previous message:**Shirley Hui: "Warning: Not all atoms have unique coordinates."**In reply to:**Shirley Hui: "cellBasisVector x,y,z values"**Next in thread:**p.w.fowler_at_qmul.ac.uk: "Re: cellBasisVector x,y,z values"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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