Re: help with how pbc are defined.

From: David Hardy (
Date: Thu Oct 11 2012 - 13:34:10 CDT


For your NAMD configuration file, using "wrapNearest" with "wrapWater" should give your DCD trajectory the appearance of the octahedron without you having to do any additional wrapping of the positions. I don't know if the PBC wrapping in VMD has the option to apply a "wrapNearest" (i.e., wrap to the image closest to the center) to an unwrapped trajectory. You probably already know that any kind of periodic wrapping is simply cosmetic and doesn't actually affect the simulation.


On Oct 11, 2012, at 12:48 PM, Martin, Erik W wrote:

> 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 … The starting structure is tip4_starting 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: However, when I used "pbc wrap" is forced everything into this box… oddly enough, when I attempted to "unwrap" the ti
p 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,
> Erik
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David J. Hardy, Ph.D.
Theoretical and Computational Biophysics
Beckman Institute, University of Illinois

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