[gmx-users] Extracting frames to a new trajectory based on RMSD cut-off value

[Sandhyaa Subramanian]

Dear all,
I have a trajectory of 10,000 frames (traj.xtc) and would like to create a new sub-trajectory (sub_traj.xtc) by extracting specific frames from traj.xtc based on certain RMSD cut-off value to the reference PDB file. For example, if my RMSD cut-off is 0.3 nm, then I would like to extract all frames from traj.xtc that have RMSD less than or equal to 0.3nm with the reference PDB file. 
Will g_cluster -f traj.xtc -s reference.pdb -n index.ndx -cutoff 0.3 -fit -o newtraj help me? I mean can I use newtraj.xpm file in the trjconv (under -sub) command to get my desired result?
Kindly help. 
Best, Sandy