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_flux is more sophisticated than g_count and gives more detailed information.
Citation: 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
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