VMD-L Mailing List
From: Rachel (comeonsos_at_googlemail.com)
Date: Wed Jul 25 2007 - 10:51:54 CDT
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Hi,
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,
Rachel
- Next message: Rachel : "how to run VMD on IBM machines"
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- Reply: Olaf Lenz: "Re: how to wrap trajectory into truncated octahedral box"
- Reply: David A. Case: "Re: how to wrap trajectory into truncated octahedral box"
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