cavity-volumes-pbc

This program calculates volume and surface area of cavities available for a given probe inside molecular dynamics models with periodic boundary conditions.

fast analytical volume and surface computation for solvent-accessible voids
uses weighted Voronoi (power) diagram / regular triangulation, works with atoms of different radii
input from GROMACS trajectory or simple text file
optional 3D mesh output for visualization of voids, STL format viewable in VMD (experimental)

Build instructions

You will need CGAL, Boost and CMake to build this software.

Quick start:

$ git clone http://github.com/a-anik/cavity-volumes-pbc.git
$ cd cavity-volumes-pbc
$ mkdir build
$ cd build
$ cmake ..
$ make

Usage

./cavity_volumes_pbc [run_control_file]

Default run control filename: cavity_volumes_pbc.inp. Sample control files can be found in the ./examples directory.

Known bugs

fails on very small and sparse configurations where periodic regular triangulation can't be built
optional/experimental 3D mesh output works only for small isolated cavities

TODO

Switch to CGAL's native implementation of periodic regular triangulations (CGAL::Periodic_3_regular_triangulation_3) available since CGAL 4.11.

Citation

S. Sastry, D.S. Corti, P.G. Debenedetti, F.H. Stillinger, "Statistical geometry of particle packings. I. Algorithm for exact determination of connectivity, volume, and surface areas of void space in monodisperse and polydisperse sphere packings", Phys. Rev. E, V.56, N5, p. 5524, 1997. doi:10.1103/PhysRevE.56.5524
Voloshin, V.P.; Anikeenko, A.V.; Medvedev, N.N.; Geiger, A., "An Algorithm for the Calculation of Volume and Surface of Unions of Spheres. Application for Solvation Shells," Eighth International Symposium on Voronoi Diagrams in Science and Engineering (ISVD), 2011, pp. 170-176. doi:10.1109/ISVD.2011.30

a-anik / cavity-volumes-pbc

readme