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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")

thermo: Chemical properties component of Chemical Engineering Design Library (ChEDL) thermo is open-source software for engineers, scientists, technicians and anyone trying to understand the universe in more detail. It facilitates the retrieval of constants of chemicals, the calculation of ... [More] temperature and pressure dependent chemical properties (both thermodynamic and transport), the calculation of the same for chemical mixtures (including phase equilibria), and assorted information of a regulatory or legal nature about chemicals. [Less]