orbeckst/orbeckst.github.com
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Discovered Sep 24, 2026
orbeckst / RecSQL
RecSQL is a hack that allows one to load table-like data records into an in-memory sqlite database for quick and dirty analysis via SQL. The SQLarray class has additional SQL functions such as sqrt or histogram defined. SQL tables can always be returned as numpy record arrays so that data can be easily handled in other packages such as numpy or plotted via matplotlib. Selections produce new SQLarray objects.
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orbeckst/pgeom
Generating atomistic models of ion channel pores as used in O. Beckstein, Philip C. Biggin and Mark S. P. Sansom, A hydrophobic gating mechanism for nanopores, J. Phys. Chem. B 105 (2001), 12902-12905 and later publications.
orbeckst/g_count
g_count and g_flux are simple Gromacs tools that are primarily useful to characterize movement of water inside a cylindrical region. This can be the pore of an ion channel or a carbon nanotube. g_count returns statistics about how many atoms of a certain type (for instance, water oxygens) occupied the region of interest. g_flux calculates the flux through a cylindrical region. g_zcoord is a dumb piece of code that just prints z-coordinates of atoms in a cylindrical region; it should be easy enough to add additional functionality. g_flux is more sophisticated than g_count and gives more detailed information but you are encouraged to check that the reported results agree with what you can see in your system. For instance, get the indices of translocating particles and then track them in a trajectory viewer such as VMD. Detailed documentation can be found in the help functions for each program (run it with -h). Background information (slighly outdated for the current g_count-gmx4.5 release) can be found in the appendix (pdf) of my thesis. When you use g_flux/g_count please cite * O. Beckstein and M. S. P. Sansom, The influence of geometry, surface character and flexibility on the permeation of ions and water through biological pores, Phys. Biol. 1 (2004), 42–52. doi:10.1088/1478-3967/1/1/005
orbeckst/gridcount
DEPRECATED and UNSUPPORTED. gridcount is an analysis tool for Gromacs that creates 3D (number) densities from molecular dynamics trajectories. Typically, this is used to look at the density of water or ions near proteins or in channels. It provides tools to generate the 3D map in portable formats, 2D cylindrical averages and 1D linear averages ("density profiles").