Gmx cluster

GROMACS version: 5.1.4
GROMACS modification: Yes

Respected Community members

I have performed a protein-ligand simulation for 200 ns using CHARMM36 forcefield using tutorials written by Dr. Lemkul. I want to cluster my entire trajectory to find out the dominant conformation of my protein with a cutoff value of 0.15 nm. I would also like to get the pdb file of the average structure from the largest cluster so that I can do some analysis on that. How can I achieve this? I read the gmx cluster documentation and assembled a command as follows:

gmx cluster -md_center.xtc -s md.tpr -n index.ndx -method gromos -cutoff 0.15 -o -g

Once prompted, I selected protein-ligand complex for least squares fitting and RMSD calculation.

The command got executed; however, and the following output was mentioned

Last frame 20000 time 200000.000

Allocated 1805702400 bytes for frames

Read 20001 frames from trajectory md_0_200_center.xtc

Computing 20001x20001 RMS deviation matrix

RMSD calculations left: 198333486

The execution took a lot of time and is still going on. Is this the correct way to perform this analysis? I am a beginner and any help would be greatly appreciated.

Thanks in advance