[gmx-users] seeking help for generating combined trajectory files and clusters

[MD]

Hi Gromacs folks,

I am trying to simulate protein and ligand compound.

I did several 200 ns simulations and combined them into one trajectory file
with the commands:
gmx trjcat -f md_round1_10-200ns.xtc
 md_round2_10-200ns.xtcmd_round3_10-200ns.xtc -o md_combined.xtc -cat
-settime
I set the starting times to be: 10 ns, 190 ns, 380 ns

Then I made a RMSD matrix with the command:
gmx rms -f md_combined.xtc -f2 md_0_1_combined.xtc -s md.tpr -n md.ndx -m
md_RMSD-matrix.xpm

Then I tried to build clusters with the command:
gmx cluster -f md_combined.xtc -s md.tpr  -n md.ndx -dm md_RMSD-matrix.xpm
-method gromos -cl out.pdb -cutoff 0.2 -g out.log

There were 120 clusters came back. Except for the first and largest
cluster, all the rest of the clusters have a crazily far away ligand
compared to where the protein is.

I went back to look at each individual xtc from each round and produced
their own clusters and they all look good (no huge separation of protein
and ligand).

If all the xtc files are good on their own, how come the combined xtc is
giving me this result?

Best,

MD