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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 Background information (slighly outdated for the current g_count-gmx4.5 release) can be found in the appendix (pdf) of my thesis.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

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