Truncated octahedron box issues (?)

From: Massimiliano Porrini (
Date: Wed May 25 2011 - 10:38:03 CDT

Dear all,

I am trying to simulate a small protein immersed in a truncated
octahedron box of water molecules.

Basically I built the box via tleap program of Amber10 and then (using
the vectors component
taken from Gromacs manual) I passed the box parameters to NAMD config
files in the
following way (the "cellOrigin" values were obtained via VMD):


# Periodic Boundary Conditions
set dist 58.9627607

set xx [ expr $dist ]
set xy [ expr $dist * 1/3 ]
set xz [ expr $dist * -1/3 ]

set yx [ expr 0 ]
set yy [ expr $dist * sqrt(2) * 2/3 ]
set yz [ expr $dist * sqrt(2) * 1/3 ]

set zx [ expr 0 ]
set zy [ expr 0 ]
set zz [ expr $dist * sqrt(6) * 1/3 ]

cellBasisVector1    $xx   $xy  $xz
cellBasisVector2    $yx   $yy  $yz
cellBasisVector3    $zx   $zy  $zz

cellOrigin          29.295766830444336 29.650468826293945 29.59993553161621


# Continuing a job from the restart files
binCoordinates     $inputname.restart.coor
extendedSystem     $inputname.restart.xsc

# Restraints
constraints         on
consref             $filename.pdb
consKfile           $filename.pdb
consKcol            O

# Periodic Images
wrapNearest         on
wrapWater           on
wrapAll             on

Hence at the end of these two processes I should get exactly the same
box shape and
dimensions as the one created via tleap (I am using an NVT esemble), but
instead, as you can see from the linked figures, the shape is different, since
the one obtained after NAMD minimization and heating appears to be "flatter":

Do you kindly have any idea/hint about this behaviour?

Should I be worried about a possible rotation of the protein and thus
a likely interaction with a periodic image of its?

Many thanks in advance.

All the best,

PS: as one can see from the displayed axes in the two enclosed figures,
the orientation of the system is exactly the same, and the "suspected
contraction" occurs along the z axis.

Dr Massimiliano Porrini
P. E. Barran Research Group
Institute for Condensed Matter and Complex Systems
School of Physics & Astronomy
The University of Edinburgh
James Clerk Maxwell Building
The King's Buildings
Mayfield Road
Edinburgh EH9 3JZ
Tel +44-(0)131-650-5229
E-mails :

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