RMSF for Center of Mass

User discussions
1

GROMACS version:2020
GROMACS modification: Yes/No
Hello,

Is it possible to calculate the RMSF with respect to the center of mass of the corresponding residue in a protein sequence?

Thank you in advance.

2

Hi
you can try to the following

  1. use gmx traj (gmx traj — GROMACS 2021.4 documentation) to transform the trajectory in a trajectory of the residue com,
  2. input to gmx rmsf the com-trajectory to calculate the fluctionation. Note that you need also to generate a gro file (for the residue-com) to input to option -s of gmx rmsf
    \Alessandra