Hi All,
Trying to learn some clustering basics using cpptraj in AMBER18.
I m trying to analyse flexible regions of my protein in explicit water simulations.
I have at present tried to do k-means clustering and this is my input file I feed to cpptraj
parm strip_XXX.prmtop
trajin XXX_stripped.mdcrd 1 last 10
cluster c1 kmeans clusters 20 randompoint maxit 500 rms :2-151.C,N,O,CA,CB&!.H= sieve 1 random out cnumvtime.dat summary summary.dat info info.dat cpopvtime cpopvtime.agr normframe repout rep repfmt pdb singlerepout singlerep.nc singlerepfmt netcdf avgout avg avgfmt pdb
run
Any ideas on “sieve” and “clusters”?
What is the optimum I should keep?
If I have no idea what should be the number of clusters should I make it 50 or 80 (a higher number) and what is the functionality of sieve I could not clearly understand from the manual.. Any suggestions?
Thanks everyone.
Regards
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Received on Tue Mar 10 2020 - 07:00:02 PDT
