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orbeckst / gridcount

DEPRECATED and UNSUPPORTED. 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").
http://sbcb.bioch.ox.ac.uk/oliver/software/#gridcount
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Support for Gromacs 4.6.x or higher #4

Open orbeckst opened 9 years ago

orbeckst commented 9 years ago

Currently gridcount does not compile against Gromacs 4.6.x (or 5.x)

With 4.6.5 the first error is

g_ri3Dc.c:107:21: error: rdgroup.h: No such file or directory
make[1]: *** [g_ri3Dc.o] Error 1
orbeckst commented 9 years ago

I don't have the time to update the code. Any patches are gratefully received and are almost certainly going to be incorporated. (Fork on github and send a pull request.)

orbeckst commented 8 years ago

Instead I suggest you look into using MDAnalysis. In particular, the MDAnalysis.analysis.density can do most of the things that gridcount was able to do. And if you have further questions, we have a very friendly and helpful mailinglist at http://help.mdanalysis.org.