VMD-L Mailing List

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Mon Jul 28 2008 - 19:50:12 CDT

sorry for being so stupid,
it just struck me that cellBasisVectors are simply rounded to higher
integer coordinate differences (max-min).

Ok, how to explain number 32???

On Mon, Jul 28, 2008 at 8:46 PM, Roman Petrenko <rpetrenko_at_gmail.com> wrote:
> 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
> 

-- 
Roman Petrenko.
Physics Department
University of Cincinnati