Unnormalised RDF

User discussions
1

Hi all,

I’m having difficulty in trying to generate an unnormalised RDF. I have used the command below but it returns with an error message.

gmx rdf -f Traj.xtc -s Input.tpr -n index.ndx -surf mol -bin 0.02 -o RDF.xvg -cn Nlig.xvg -seltype mol_com

So as you can see I want to calculate the unnormalised RDF between my protein and COM ligand. In the error message it says -ref should contain atoms. My index file does contain atoms e.g. it says there are 6615 atoms in the group but it does not seem to work. Please may someone guide me in solving this problem?

Akash

2

Hi,
The option -surf can be combined only with atom as seltype. In alternative you can calculate the RDF between com protein and com ligand, it depends what you are interested in.
Best regards
Alessandra

3

Thank you for your reply. This may sound like a simple question but what’s the difference between the number density and the g® in Gromacs?