[gmx-users] RDF Values

Pandya, Akash akash.pandya.15 at ucl.ac.uk
Mon Jul 31 09:29:22 CEST 2017

Hi all,

I am calculating the RDF from a particular residue to a particular glycine molecule. I created an index file for both to do this. My simulation box is 1.5nm, but the RDF values are in the range of 2nm-3nm. I have viewed my trajectory and all the components stay inside the box. Please could someone tell me how to overcome this issue? My command line is below:

gmx rdf -f output.xtc -s input.tpr -n index.ndx -o rdf.xvg -b 0 -e 60000 -ref -sel -bin 0.5 -norm rdf


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