RDF between atoms in lipids, but without atoms from the same lipid molecule

GROMACS version: 2018.4
GROMACS modification: No
I have a question. I want to calculate RDF oxygen atoms in carbonyl groups with the respect to oxygen in digalactose residues. I have a membrane which consists of 200 DGDG molecules. The problem with RDF is that in gromacs it calculates also between atoms in the same molecule, I don’t want that. I want to calculate RDF for atoms from different molecules, no for example between 2 oxygens in the same molecule

I created two index groups 1) for oxygen in carbonyl groups, 2) for oxygen in digalactose residues and I used gmx rdf
gmx rdf -f eq3.xtc -n rdf.ndx -b 900000 -e 1000000 -rmax 1 -o rdf_O22_O32_GalI_II_DGDG.xvg

what I should change?

gmx rdf calculates radial distribution functions from one reference set of position (set with -ref ) to one or more sets of positions (set with -sel ). Then when the two groups are defined without overlapping (common) elements, the tool is doing what you want.
Or I misunderstood your question?
Best regards

1 Like