[gmx-users] Wrapping molecules for octahedron box

Mark Abraham Mark.Abraham at anu.edu.au
Wed May 12 05:38:50 CEST 2010

On 12/05/2010 2:27 AM, Sai Kumar Ramadugu wrote:
> 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

Never heard of "aninit" and it's not in GROMACS.

> 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?

There are various functions that deal with periodic boundary conditions. 
Search for pbc in the code.


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