[gmx-users] Selection Error for RDF calculations

Pandya, Akash akash.pandya.15 at ucl.ac.uk
Tue Dec 12 23:12:42 CET 2017

Hi all,

I am trying to calculate the RDF in system with my protein and also glycine. I have made a custom index groups for the protein and also the glycine as show below:

> ri 1-442

Found 6615 atoms with resind.+1 in range 1-442

24 r_1-442             :  6615 atoms

> ri 466-619

Found 1540 atoms with resind.+1 in range 466-619

25 r_466-619           :  1540 atoms

When I type in the appropriate command:

gmx rdf -f protein_gly.gro -n protein_gly.ndx -b 0 -e 60000 -tu ns -o rdf.xvg -norm rdf -bin 0.2

I get the following error when I finish selecting the 'ref' which is the protein and `sel` which is the glycine molecules

Inconsistency in user input:
Invalid index group references encountered
  Group 'r_466-619' cannot be used in selections, because it contains negative
  atom indices and/or references atoms not present (largest allowed atom index
  is 8155).

Please can someone advise me on what I should do?


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