Overview

trjVoronoi computes the atomic Voronoi volumes and surfaces of a molecular dynamic trajectory written in .dcd or .xtc format. It requires a .pdb file containing the coordinates of the whole system, including waters and ions. The code uses voro++ by Chris H. Rycroft to compute properties of molecular systems in solution from molecular dynamics trajectories obtained with GROMACS and NAMD. To download the code please go to the Download page.

Distribution

trjVoronoi is distributed with a GNU compatible license and can be downloaded from the download page.

How to cite trjVoronoi:

Please consider first citing the Voro++ code with one of the three references:

• Chris H. Rycroft, Voro++: A three-dimensional Voronoi cell library in C++, Chaos 19, 041111 (2009).
• Chris H. Rycroft, Gary S. Grest, James W. Landry, and Martin Z. Bazant, Analysis of Granular Flow in a Pebble-Bed Nuclear Reactor, Phys. Rev. E 74, 021306 (2006).
• Chris H. Rycroft, Multiscale Modeling in Granular Flow, PhD thesis submitted to the Massachusetts Institute of Technology, September 2007.

Then consider citing our Work:

• S. Abel, F. Y. Dupradeau and M. Marchi "Molecular Dynamics Simulations of a Characteristic DPC Micelle in Water" J. Chem. Theory Comp. 8, 4610-4623 (2012)