Re: cellBasisVector x,y,z values

From: p.w.fowler_at_qmul.ac.uk
Date: Thu Jul 08 2004 - 10:30:31 CDT

These are the lengths of the sides of the unit cell. So if your unit cell were
100Ax50Ax60A then the cellBasisVectors would be

cellBasisVector1 = 100,0,0
cellBasisVector2 = 0,50,0
cellBasisVector3 = 0,0,60

An important point is to make sure that your system is centred on the origin:
NAMD assumes this.

--Phil

> 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 = 42, y = 0, z = 0. With each vector
> perpendicular, a rectangular 3-D box is formed."
>
> http://www.ks.uiuc.edu/Training/SumSchool/materials/sources/tutorials/02-na
>md-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

-- 
Philip Fowler, 
PhD Student
Centre for Computational Science,
UCL Chemistry

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