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
Hi, 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
Alessandra
Dear sir, i met a problem like the following.
GROMACS version:2023.1
GROMACS modification: No
Here post your question
hi,everyone,
i have a micelle composed of 40 molecules A, and i have a drug molecule B. i wang to caculate the rdf function between the center of mass (com) of the micelle and drug B, but i can not get a proper result.( the drug was on the surface of the miclle ,but the rdf was not right.
my rdf is caculated by :
gmx rdf -f trajout.xtc -s md.tpr -ref “com of group A” -sel “com of group B” -pbc -bin 0.1