AMBER Archive (2004)

Subject: AMBER: question about image - truncated octahedron

From: Chris Moth (chris.moth_at_vanderbilt.edu)
Date: Sat Apr 03 2004 - 09:22:14 CST

>===== Original Message From "Thomas E. Cheatham, III"
<cheatham_at_chpc.utah.edu>
>If your analysis program is set up to correctly image distances, angles,
>etc, there should be no difference before and after imaging...

This discussion thread reminded me of a issue I need to address in my own
code.

If you know of any references along the lines of

"(Complete) Periodic Imaging of Truncated Octahedra for Dummies" :)

they would be appreciated.

Details:

Our MD trajectory visualiztion tool MDDisplay images atoms
back into a rectangular box just fine.

Recently, I've upgraded it to image into truncated octahedra using these
helpful references:

--------------------------------------------
Allen, M.P.; Tildesley, D.J.; Computer Simulation of Liquids, Oxford
University Press, 1987
Specifically, see appendix F program F.1 (found at various web sites)
--------------------------------------------
van Gunsteren - lecture notes on MD simulation page 10-11:
 www.chem-edu.ethz.ch/rosm/docs/rosm01-6.pdf
--------------------------------------------

But, my octahedron code is not quite complete. Solvent atoms
wind up in funny places (in and around the protein core) from time to time -
though all atoms are certainly in the truncated octahedron. I've tried to
sift through the general imaging code in ptraj.. but it is not entirely clear
to me how that is working.

(This bug is mainly a nuisance - the misplaced solvent atoms pop in and out,
and are easy to distinguish from correctly placed structural waters around the
protein car).

I've also tried to extrapolate the code from the various AMBER references on
periodic simulations. These are not very direct either, in my experience so
far.

Thanks very much for any suggestions.

Chris Moth
http://www.structbio.vanderbilt.edu/~cmoth/mddisplay

Chris Moth
chris.moth_at_vanderbilt.edu

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