[gmx-developers] upload: gridcount

Oliver Beckstein oliver at biop.ox.ac.uk
Thu Mar 18 02:00:40 CET 2004


I added some analysis code to the contributions page. Basically, it just 
counts atoms or molecules on a grid and creates a 3D density (time 
averaged). Once the 3D density file is written it can be analysed with the 
accompanying analysis tool or exported into the gOpenMol plt format 
(thanks to Christoph Freudenberger for code snippets to do that). 


g_ri3Dc grid-counts atoms or molecules from an index file and writes a 3D
density file (portable xdr format). The analysis tool a_ri3Dc reads the 3D
density and can convert it into gOpenMol's plt format (can be imported
into VMD), ascii dump, or it can do 2D slices (in xfarbe
http://www.fhi-berlin.mpg.de/grz/pub/xfarbe/ format) or cylindrical
averages (see these examples
), useful for looking at ion channels. See the README for compilation
instructions (tested with Gromacs 3.1.4 and 3.2.1).


Oliver Beckstein * oliver at biop.ox.ac.uk

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