GMX Cluster is not giving RMSD distributions that make sense?

User discussions
1

GROMACS version: 2019.4
GROMACS modification: Yes (with MPI)

I was hoping to get some help on the gmx cluster command. When I use the -s struct.pdb flag, no matter what reference frame I input, I get the same RMSD distribution. As a sanity check, I looked at the RMSD distribution (RMSD vs. time) on VMD, and the RMSD distribution did not really correlate with what I saw in my gmx cluster output. Here is a sample of my gmx cluster command:

gmx_mpi cluster -f ./trajectory.xtc -s ./ref-struct.gro -dist ./somefolder/rmsd-distribution.xvg -o ./somefolder/clusters.xpm -sz ./somefolder/cluster-sizes.xvg -tr ./somefolder/cluster-transitions.xpm -ntr ./somefolder/cluster-transitions.xvg -clid ./somefolder/cluster-id-over-time.xvg -cl ./somefolder/clusters.pdb -cutoff 0.25 -method gromos -n …/…/index.ndx -skip 10 -b 0 -e 153200

Am I misinterpreting what -dist is supposed to output? To me, it makes more sense that by changing my reference structure, ref-struct.gro, the RMSD distribution should also change.

2

Quick bump to the thread! Still confused. Thanks for the help.

3

Hi,
I guess it depends if the clustering approach depends or not from the reference structure. I think gromos approach does not, but you can check: the algorithm is described in Daura et al. ( Angew. Chem. Int. Ed. 1999 , 38 , pp 236-240).

Best regards
Alessandra

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4

I see, thank you for clarifying! I’ll have to re-read the paper again to make sure I fully understand how the GROMOS algorithm works.