**From:** Kamp, Marc vander (*Marc.vanderKamp_at_wur.nl*)

**Date:** Thu Jul 08 2004 - 10:18:42 CDT

**Next message:**p.w.fowler_at_qmul.ac.uk: "Re: cellBasisVector x,y,z values"**Previous message:**Edward Patrick Obrien: "Re: cellBasisVector x,y,z values"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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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