search

orbeckst / g_count

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 Background information (slighly outdated for the current g_count-gmx4.5 release) can be found in the appendix (pdf) of my thesis.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
Other
8 stars 1 forks source link

Gromacs 5.1.2 #6

Open scinikhil opened 8 years ago

scinikhil commented 8 years ago

Gromacs 4.XX is very older version ,what is the possibility for latest gromacs versions or gromacs 5. xx

orbeckst commented 8 years ago

Sorry, I don't have the time to update the code for newer Gromacs versions. I am more than happy to merge pull requests in case you want to have a go at it.

scinikhil commented 8 years ago

I think it will be helpful for many if you can update it or anything can implement with 5.X Since 4.5X outdated

Personally, my interest is in study the permeation ,conductivity and flux of many bio-nanotubes . Thanks