VMD-L Mailing List

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Mon Jul 28 2008 - 19:46:09 CDT

Dear all,
after looking at the namd tutorial and the user guide and still do not
understand how to come up with the numbers for periodic boundary
conditions!
---------------------
># Periodic Boundary Conditions
>cellBasisVector1 42. 0. 0.
>cellBasisVector2 0. 44. 0.
>cellBasisVector3 0. 0 47.
>cellOrigin 31. 29. 17.5
>wrapAll on
># PME (for full-system periodic electrostatics)
>PME yes
>PMEGridSizeX 32
>PMEGridSizeY 32
>PMEGridSizeZ 32
-----------------------
The only line i understand here is cellOrigin, which i compute as
set cen [measure center [atomselect top "all"] weight mass]
cellOrigin [lindex $cen 0] [lindex $cen 1] [lindex $cen 2]

BUT, how to find all other magic numbers 42,44,47, and 32 for specific protein?

Please, help 

-- 
Roman Petrenko.
Physics Department
University of Cincinnati