I used cubic box before, but it had too many water molecules for big system. Truncated octahedral could reduce 50% size of the overall system.

I got two solutions for this. To visualize the box correctly, add **wrapall on** and **wrapnearest on** in your configuration file.

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The first solution was got from http://nefeli.mbg.duth.gr/cgi-bin/wiki.pl?action=browse;diff=1;id=Performing_a_molecular_dynamics_simulation_in_a_truncated_octahedral_cell.

In the *NAMD* scripts you will have to define the unit cell translations for the truncated octahedron (the *cellbasis* keywords). The matrix you need is

d |
0 | 0 |

0 | d |
0 |

d/2 |
d/2 |
d/2 |

where *d* is the length of the edge of the cube you’ve specified in the *vmd* script. For the example shown above you would have to specify

cellBasisVector1 32.00 0.00 0.00 cellBasisVector2 0.00 32.00 0.00 cellBasisVector3 16.00 16.00 16.00 cellOrigin 0.00 0.00 0.00

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The second solution was got form http://ambermd.org/namd/namd_amber.html.

## Truncated Octahedron (TO)

*d*is the length of the edge of the TO, than the three vectors should be:

cellBasisVector1 d 0.0 0.0 cellBasisVector2 (-1/3)*d (2/3)sqrt(2)*d 0.0 cellBasisVector3 (-1/3)*d (-1/3)sqrt(2)*d (-1/3)sqrt(6)*d

d d d 109.4712190 109.4712190 109.4712190 ------------------------------------------------------