On May 21, 2014, at 3:19 PM, Eugene Yedvabny <eyedvabny.berkeley.edu> wrote:
> Hello Amber community,
>
> I was wondering if cpptraj has a functionality for calculating
> intermolecular contacts across periodic boundaries. I am doing simple
> single-protein-in-a-water-box simulation and am curious if any of the
> protein residues are influenced by residues *from the periodic images *(to
> make sure the water box is large enough)*. *Such analysis is trivial enough
> to do outside of AMBER for a rectangular box, but I am using a truncated
> octahedron, and so was wondering if this functionality already existed?
You'll need to define "influenced". As Dan mentioned, many (most?) actions in cpptraj that compute distances between pairs of atoms automatically take care of imaging (although that can be disabled in many cases with a keyword like "noimage").
One limitation (which is pretty much a limitation everywhere) is that the minimum image convention is obeyed, so only the closest image will be computed. If you just want to make sure that closest image of every atom in your protein to every other atom in your protein is in the same molecule (e.g., the "top" of your protein is closest to the "bottom" of the same protein and not the bottom of the protein in the box above), then the "distance" or "nativecontacts" commands in cpptraj can be coerced into providing the information you want.
If, on the other hand, you want to actually try and quantify the interactions of the periodic images, you will need to do something a bit more sophisticated -- basically compute the energy of the protein without periodic boundaries and subtract that from the energy of the protein _with_ periodic boundaries all while the water charges/vdW parameters were set to zero (and forces, too, if you are interested in those as well).
I think a more "typical" indication that your box is "big enough" is whether or not water eventually mimics bulk behavior when you get far enough away from the protein. If your box is too small, this cannot happen (since the water is never far enough from some periodic image of the protein to decorrelate). You can compute a radial distribution function for this (which again takes periodic boundaries into account in the cpptraj implementation).
Hope this helps,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed May 21 2014 - 15:00:03 PDT
