Gmx traj for center of mass

User discussions
1

GROMACS version: 2018
GROMACS modification: No

Dear all,
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!

Kind regards
Alex

2

Hi Alex,

You should be able to leverage the selection syntax in gmx trajectory (not gmx traj) to give you what you want by specifying com of ATOM_EXPR [pbc] (didn’t try myself though)

Have a look here:

3

Thanks Cblau,
My attempt to assign a right selection in “gmx trajectory -select … -n index.ndx …” to produce what I need is unsuccessful.

In my index file I have a group called [ A ] where A contains 1000 molecules. What I need is to print out the xyz_COM of each of those 1000 molecule versus simulation time in a single file.
The -select ‘com of ATOM_A’ does not work in gmx trajectory.
Would you please let me know how that selection should be?

Thank you.