Cluster Analysis without a trajectory file

GROMACS version: 2018.4
GROMACS modification: No
Here post your question
I conducted simulated annealing 30 times in a loop and it generated 30 structures. Is there a way to do cluster analysis on these final 30 structures instead of using a trajectory file as input for gmx cluster?

gmx accepts one of the follow as options to specify for input files:

-f [<.xtc/.trr/…>] (traj.xtc) (Optional)

Trajectory: xtc trr cpt gro g96 pdb tng

Just to add on to the previous answer, you can always make a trajectory file by feeding your .gro configurations to gmx trjcat:

  1. Error on using gmx trjcat with a gro file as input:
    It can only handle binary trajectory formats (trr, xtc, tng)

  2. Question: Is there a way to use multiple gro files as input and convert them all into a single trr file? And then use that as input for gmx cluster?

Apologies, it looks like there was some misleading documentation for trjcat (see: You will have to convert each .gro to .xtc using trjconv and then concatentate.

While possible, this is unnecessary; since .gro and .pdb files are just text, use the standard Linux cat command to make the multi-frame “trajectory” file.

cat *.gro > traj.gro