Dear List,
I have 1 microsecond trajectory and each frame is saved every 10 ps. I
m using following command to perform clustering analysis
trajin prod1.mdcrd 1 1000 1
trajin prodX.mdcrd 1 1000 1
strip :WAT
strip :Cl-
strip :Na+
cluster hieragglo epsilon 4 averagelinkage rms.CA sieve 10 out
cnumvtime summary summaryfile clusterout clus clusterfmt amber repout
repclus repfmt pdb
I get following warning:
Warning: [cluster] Not all arguments handled: [ sieve 10 ]
Is the syntax correct? I am using averagelinkage since I don't know
the total number of clusters in the final outcome. Is the above syntax
doing clustering based on Calpha atoms? Since processing 10000 frames
is time consuming, I thought I would use sieve to use less number of
frames for clustering.
Your guidance is appreciated.
Regards,
Neha Gandhi
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Received on Thu Dec 26 2013 - 03:30:03 PST
