Molecular Dynamics wrote:
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.
Have you tried typing "help" at the make_ndx prompt? You'll get tons of
information, including the commands needed to create the groups you want.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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