Clustering of a protein with 2 chains

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Hi Guys,

I just finish a production run of a protein with two chains (chain A and chain B)
and have corrected the trajectories with trjconv
upon visualization with vmd there seems nothing wrong with the protein as both chains stay at it own position along the 50 ns run
however, after i do gmx cluster for clustering analysis, some of the cluster conformation showed that the chain A and chain B are separated
the command i used is
(gmx cluster -s md_50.tpr -f md_ml.xtc -method gromos -g cluster.log -cutoff 0.6 -n index.ndx -cl cluster.pdb) where -n is the index of chain A and chain B
is there any way to get the cluster conformations without the chains become separated?

I guess you refer to the structures saved in cluster.pdb and that those structures show chain A and chain B not close to each other.
Did you use the post-processed trajectory as input of gmx cluster?
I think that the structures saved in cluster.pdb are taken from the given trajectory.

Hello @syaripn3ds and @alevilla
Actually I have a doubt. I wanted to know how to extract the trajectory using trjconv. Because I am working on a dimer and I am stuck at extraction of trajectory because one method shows the chains near and another shows the chains away. I am not sure whether they are really separated or are just the periodic images at far end of the box as visualized on VMD.

And I also wanted to know whether we can do clustering based on distance between chain A and B in the trajectory, so that I can know if the chains have separated.