From: Shirley Hui (shirleyhui_at_alumni.uwaterloo.ca)
Date: Thu Jul 08 2004 - 08:46:16 CDT
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
> 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."
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
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:18:19 CST