[gmx-users] RDF Values

saima kalsoom genious_chemist at yahoo.com
Mon Jul 31 10:08:01 CEST 2017

hi dear!can anyone please suggest me what does it mean."In chosen Force field there is no residue type for QLN"there was no QLN in our origin file. There is always a problem when i select any force field.regards 

    On Monday, 31 July 2017, 12:29, "Pandya, Akash" <akash.pandya.15 at ucl.ac.uk> wrote:

 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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