# RE: cellBasisVector x,y,z values

From: Kamp, Marc vander (Marc.vanderKamp_at_wur.nl)
Date: Thu Jul 08 2004 - 10:18:42 CDT

To get the correct dimensions of the box you should take the difference between the minimum and maximum values, you want to determine and set your box size in the x, y and z direction of course!
(The values for the cellBasisVectors should be somewhat larger than measured box-size to add some extra space to your system's bounding box since each atom's radius will wrap around.)

good luck,
Marc

-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu on behalf of Shirley Hui
Sent: Thu 8-7-2004 15:46
To: namd-l_at_ks.uiuc.edu
Cc:
Subject: namd-l: cellBasisVector x,y,z values

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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