From: Martin, Erik W (Erik.Martin_at_stjude.org)
Date: Thu Oct 11 2012 - 12:48:27 CDT
I've been using orthogonal boundary conditions for ages, and thought I had a good handle on how this worked. However, I recently had to start using a truncated octahedron and its become a bit of a mystery to me. I followed what instructions I could find and defined my basis vectors as:
vector1 d 0 0
vector2 -1/3d 2/3sqrt(2) d 0
vector3 -1/3d -1/3sqrt(2)d -1/3sqrt(6)d
Or specifically in my case:
periodic cell dcdUnitCell yes cellBasisVector1 110.906 0.0 0.0 cellBasisVector2 -36.9688 104.5635 0.0 cellBasisVector3 -36.9688 -52.2818 -90.5547 cellOrigin 0.0 0.0 0.0
The first structure I started appears to be running just fine. However, I left the line "wrapWater" out of the configuration file. When I set up a second structure (all I changed was the water model to tip4) I included this line. The simulation changed the structure to some manner of parallelogram (see attached picture tip4_box1 http://dl.dropbox.com/u/54597523/tip4_box1.jpg … The starting structure is tip4_starting http://dl.dropbox.com/u/54597523/tip4_starting.jpg). I visualized the PBC with "pbc box" and saw that this was the shape of my boundary conditions – albeit shifted. There appeared to be no error in the running of the simulation, just this change. When I went back and looked at the tip3 simulation, I found that the shape of the boundary condition was the same, but seemed to have no impact on the structure (picture tip3_box1: http://dl.dropbox.com/u/54597523/tip3_box1.jpg). However, when I used "pbc wrap" is forced everything into this box… oddly enough, when I attempted to "unwrap" the tip
4 simulation it didn't return to the truncated octahedron.
Is there something I'm missing here about how the boundary conditions are defined in the case of a truncated octahedron? Have I done something wrong? Perhaps its simply not possible to use wrapWater with this type of symmetry?
Thanks a lot for any help,
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