VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Jul 28 2008 - 20:44:41 CDT

On Mon, 28 Jul 2008, Roman Petrenko wrote:

RP> sorry for being so stupid,
RP> it just struck me that cellBasisVectors are simply rounded to higher
RP> integer coordinate differences (max-min).
RP>
RP> Ok, how to explain number 32???

about one gridpoint per angstrom? that is typical
for PME with normal accuracy.

if you start from the result of "solvate" it doesn't
really matter if your box is too large (but too small
will get you into trouble due to overlapping atoms).
running in NPT-ensemble will then shrink the box to
normal density. from then on you'd either restart or
have to fix your input.

cheers,
   axel.

p.s.: this is namd-l stuff, right?

RP>
RP>
RP>
RP> On Mon, Jul 28, 2008 at 8:46 PM, Roman Petrenko <rpetrenko_at_gmail.com> wrote:
RP> > Dear all,
RP> > after looking at the namd tutorial and the user guide and still do not
RP> > understand how to come up with the numbers for periodic boundary
RP> > conditions!
RP> > ---------------------
RP> >># Periodic Boundary Conditions
RP> >>cellBasisVector1 42. 0. 0.
RP> >>cellBasisVector2 0. 44. 0.
RP> >>cellBasisVector3 0. 0 47.
RP> >>cellOrigin 31. 29. 17.5
RP> >>wrapAll on
RP> >># PME (for full-system periodic electrostatics)
RP> >>PME yes
RP> >>PMEGridSizeX 32
RP> >>PMEGridSizeY 32
RP> >>PMEGridSizeZ 32
RP> > -----------------------
RP> > The only line i understand here is cellOrigin, which i compute as
RP> > set cen [measure center [atomselect top "all"] weight mass]
RP> > cellOrigin [lindex $cen 0] [lindex $cen 1] [lindex $cen 2]
RP> >
RP> > BUT, how to find all other magic numbers 42,44,47, and 32 for specific protein?
RP> >
RP> > Please, help
RP> >
RP> > --
RP> > Roman Petrenko.
RP> > Physics Department
RP> > University of Cincinnati
RP> >
RP>
RP>
RP>
RP> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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If you make something idiot-proof, the universe creates a better idiot.