[gmx-users] COM motion removal: diffusion analysis

[gromacs query]

Hi All


I have protein-membrane system and gromacs tutorial by Justin suggests to
do COM separately for protein_membrane and water. I am bit meesed up COM
removal understanding.


1) I want to do diffusion analysis of protein in a membrane (2D/3D) how it
will influence my results if I perform it on a trajectory with COM removal
as seperate groups or on trajectory with COM removal of system.

2) Is it possible to remove COM seperately on a trajectory created using
COM removal on system. e.g. for msd calculation one can use -rmcomm

3) May be am wrong here: In case of simple peptide in water box, and I
remove COM for peptide and water (NOT as whole system) then in this case
peptide should not cross the unit box. Is it right?


Thanks for any help
J