From: Rachel (
Date: Wed Jul 25 2007 - 10:51:54 CDT


I am using VMD to view the trajectory files from AMBER with truncated
octahedral water box, as i need to image the trajectories into the primary
box which I used pbctools in VMD.

The angles between the XY and YZ planes are 109.47, and box lengthes are
93.30 in XYZ directions, so I used:
pbc set {93.3 93.3 93.3 109.47 109.47 109.47} -all

However, this gave me a pallelepiped periodic box instead of octahedral box.

Can anyone tell me how to wrap the trajecotries into a truncated octahedral
box? thank you for your help.

Kind regards,