GROMACS version: 2019.1
GROMACS modification: No
Hello Gromacs users,
Two dominant clusters (red and blue regions in the plot below) were extracted from the trajectory using rmsd clustering. I was wondering is there a command that I can use in gmx cluster to automatically generate cluster specific trajectory files?
Thank you,
Neena
Hi,
Maybe the option -cl is the closest to what you want. The option -cl writes average (with option -av ) or central structure of each cluster or writes numbered files with cluster members for a selected set of clusters (with option -wcl , depends on -nst and -rmsmin ). The center of a cluster is the structure with the smallest average RMSD from all other structures of the cluster.
As default it generate a pdb file, but one should be able also to generate xtc file.
\Alessandra
Thank you Alessandra!
With -cl aaa.xtc command, I just get one output trajectory. Say I have 4 clusters, is there a way to get 4 cluster specific trajectories using gmx cluster? Some clusters are not continuous in time for example the red trace as shown above in the trajectory. I need cluster specific xtc files to extract H-bond occupancy from each cluster.
Hi,
you can try to combine the option -cl with the following option
-wcl (0)
Write the structures for this number of clusters to numbered files
-nst (1)
Only write all structures if more than this number of structures per cluster
I hope it helps
\Alessandra
Thank you so much Alessandra!
Yes -wcl option worked very well and generated cluster specific trajectory. This is a huge time saver.
Thank you again!
(A struggling graduate student)