GROMACS version:2023.1
GROMACS modification:No
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Dear everyone，
i have a micelle composed of 40 molecules A, and i have a drug molecule B. i want to calculate 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 micelle ,but the rdf was not right.
my command line is :
gmx rdf -f trajout.xtc -s md1.tpr -n index.ndx -ref “com of group A” -sel “com of group B” -bin 0.03
how should i do next .
thank you in advance.