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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…
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 i…
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_c…
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), 12902-12…
Old Python scripts and libraries to analyze the simulations in Beckstein et al, J Mol Biol 394 (2009), 160.
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