Hi…
I used gmx clustering command line, which generated clusters.pdb file. When I opened the file in PyMOL, it had cluster 1 with 70 structures and cluster 2 with 1. As I understand it, cluster 1 contains all selected frames, and cluster 2 contains the middle structure, and we should consider cluster 2 for further analysis. Please give me some clarification regarding this.
Also, cluster.pdb file is very large to open, it’s approximately 5170469 KB. That’s why I want to extract only the middle cluster image from cluster.pdb. which will be easy to handle. Please provide some suggestions to implement this approach.
Here is the command that I used:
gmx cluster -s md_0_1.tpr -f md1.xtc -cutoff 0.30 -method gromos -g -cl
Here is the file opened in PyMOL.
give me your valuable suggestions.
Thankyou.