[gmx-users] query about g_rdf and make_ndx

sangeeta kundu sangeeta0983 at yahoo.co.in
Tue Feb 20 15:01:58 CET 2007

Dear All,
        I want to calculate the rdf of a particular residue with respect to water, I was able to generate the rdf of the entire protein against the bulk water,but I could not do the same  for a particular residue, In the index.ndx file I have specified the groups of that particular residue, but how can I correlate it with the bulk water ? 
            I think I should generate an .ndx file with  all the atoms I need as well as the solvent molecules, but I have some basic problem in understanding the preparation of .ndx file, when I am executing the commnad make_ndx and select system, index file is being prepared, but there I can not specify groups , everytime  it is said that group is empty, I am doing some mistake , but can not detcet it, please help in this two matters.

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