[gmx-users] make_ndx and rdf

Molecular Dynamics moleculardynamics at yahoo.com
Mon Oct 3 16:13:24 CEST 2011

Dear All,

I want to calculate rdf for carbon-oxygen, carbon-hydrogen and carbon-water using g_rdf but how can I generate an .ndx file that are suitable for these systems ? I searched mailing list and read manual but couldn't generate .ndx file using make_ndx tool. However, I tried to see the make_ndx examples in gromacs wiki page but couldn't reach the wiki page. Could you please help me about generating .ndx file  ? 

Carbon in group 1
hydrogen in group 2
oxygen in group 2
group 2 is water

I will be gratefull for your helps. 

All the best.
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