Truncated octahedral cell in NAMD.

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)

To use a TO in sander/pmemd you have to use the solvateOct command in tleap/sleapm, or to modify the last line of the crd/rst file to the corresponding values. NAMD will not read the box information from the crd/rst file generated from tleap/sleap. Instead you will have to specify the box information using the cellBasisVector1, 2, 3. If the 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
The last line of your crd/rst file gnerated from tleap/sleap or from sander/pmemd should look like:
d d d 109.4712190 109.4712190 109.4712190
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