COM of micelle

User discussions
1

GROMACS version: 2021.3
GROMACS modification: No

I have run a simulation looking into the micelle formation by a surfactant using 10-60 molecules in a bix. I would like to study the distribution of different atoms from the micelle core.

Looking into papers, I found that most groups have studied distance of different atoms of surfactant from COM of micelle. I assume “gmx rdf” will be used here. However, I could not figure out how to do that? The reference group can be defined with an index file. So, should I just take all molecules in the micelle as my selection group and Gromacs will itself calculate COM. Or, is there any other way?

Regards,
Raman

2

I am also confued about that.
the following seems right.
gmx rdf -f trajout.xtc -s md.tpr -ref “com of group A” -sel “group B(your atoms)” -pbc -bin 0.1

my problem is that /(ㄒoㄒ)/~~
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.