[gmx-users] Wrapping molecules for octahedron box

Sai Kumar Ramadugu sramadugu at gmail.com
Tue May 11 18:27:33 CEST 2010

Dear Gromacs Users,
   I have a simulation of a protein in Truncated Octahedron box. I want to
calculate the water residence times and mean square displacements (of water)
around the active site residues. We developed our own algorithm for doing
the same.
In earlier simulations I had cubic box and anint() function was working for
the periodic boundary conditions. Now that I have truncated octahedron box,
is there any function to my rescue? I searched the gromacs forum and could
not find any function. Is there any way to circumvent this problem?

Sorry if this is a repost.

Thanks for your time.

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