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. Regards Ying-Hua
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