GROMACS version: 2018
GROMACS modification: No
I wonder how to extract the center of mass of individual molecules of a specific group along the trajectory? I am looking for something similar to what “gmx traj -ox” gives out for a group (contains several molecules) of selection, but rather to have COM(x y z) of each molecule print out instead of position of individual atoms of the molecules. A file likes:
t_0 com_x_mol1 com_y_mol1 com_z_mol1 com_x_mol2 com_y_mol2 com_z_mol2 com_x_mol3 com_y_mol3 com_z_mol3
t_1 com_x_mol1 com_y_mol1 com_z_mol1 com_x_mol2 com_y_mol2 com_z_mol2 com_x_mol3 com_y_mol3 com_z_mol3
Of course one option is to have each individual single molecule as a group in index file and then “gmx traj -com -ox” can offer a file for each molecule which needs then to paste the files beside each other, but that is a really tedious when several hundreds of molecules are involved.
I also tried to consider the -mol flag likes “gmx traj -com -mol -ox”, but some weird numbers got printed out. I am not just sure if the -mol flag is meant to do what I want!