VMD-L Mailing List

From: Balazs Jojart (jojartb_at_pharm.u-szeged.hu)
Date: Tue Jul 29 2008 - 01:21:17 CDT

Hi Roman,
look the folllowing link:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/0051.html
hope this helps.
balazs

Roman Petrenko wrote:
> 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
>>
>>
>
>
>
>