Calculate distance between each residue and center of mass of the protein for all frames

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Hello,
I would like to calculate the distance between the Cα atoms (each C-alpha) to the geometric center of the protein in each snapshot. How can I do it using Gromacs?

Thank you.

2

Hi,
maybe you can look at gmx pairdist gmx pairdist — GROMACS 2022.1 documentation
\Alessandra

3

The article On the in silico application of the center-of-mass distance method, published in Gene & Protein in Disease, may help you solve your problem.