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 Background information (slighly outdated for the current g_count-gmx4.5 release) can be found in the appendix (pdf) of my thesis.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
I am trying to compile "g_count-gmx4.0-6.tar.bz2" with gromacs-4.0.2, but after editing makefile when I used "make check" command it ended with the the following error:
OK Gromacs include directory found: /usr/local/gromacs/include/gromacs
Even though the code was changed to compile against Gromacs 4.5.3, it appears that g_flux produces non-sensical results (e.g. lists waters as crossing that don't).
The release naming scheme underwent a number of iterations, and in part is driven by changes in the Gromacs code base. For instance, g_count had to be altered between Gromacs 4.0.x and 4.5.x.
At time of writing, the current stable release is release-gmx4.0-6 (which compiles against Gromacs 4.0.x).
The current naming scheme looks like "release-gmx<GROMACS_MAJOR>.<GROMACS_MINOR>-<GCOUNT_RELEASE>" where <GCOUNT_RELEASE> is an integer that just gets increment independently from the Gromacs releases.
Older schemes used "release-gmx<GROMACS_MAJOR>.<GCOUNT_RELEASE>"; unfortunately, that looks almost like the new scheme.
Very old: something like "release-0.3" – don't use those anymore (they compile against various version of Gromacs 3.x)
The last number is always a <GCOUNT_RELEASE>, so look at that and then deduce the Gromacs release by looking at anything left of the <GCOUNT_RELEASE>.
Not able to linking the g_count file from the installation folder to the usr/local/gromacs/bin folder.
I use similar commands as indicated in the INSTALL file.
I am using the current version of g_count with Gromacs-4.5.5 version.
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