parm ATGonium__dry13.prmtop
parm ATGonium_dry13.prmtop
trajin ATGonium_dry13.ann.traj
cluster C0 dbscan minpoints 25 epsilon 0.9 sievetoframe rms :1-10 sieve 10 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 restart
run
> parm ATGonium_dry13.prmtop
	Reading 'ATGonium_dry13.prmtop' as Amber Topology
	Radius Set: modified Bondi radii (mbondi)
> trajin ATGonium_dry13.ann.traj
	Reading 'ATGonium_dry13.ann.traj' as Amber Trajectory
> cluster C0 \
        dbscan minpoints 25 epsilon 0.9 sievetoframe \
        rms :1-10 \
        sieve 10 \
        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 restart
    CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask [:1-10]) best-fit
	DBSCAN:
		Minimum pts to form cluster= 25
		Cluster distance criterion= 0.900
		Sieved frames will only be added back if they are within
		  0.900 of a frame in an existing cluster.
		  (This option is more accurate and will identify sieved
		  frames as noise but is slower.)
	Initial clustering sieve value is 10 frames.
	Only non-sieved frames will be used to calc within-cluster average.
	Cluster # vs time will be written to cnumvtime.dat
	Cluster pop vs time will be written to cpopvtime.agr (normalized by frame)
	Pairwise distance data set is 'C0[PWD]'
	Cluster information will be written to info.dat
	Summary of cluster results will be written to summary.dat
	Representative frames will be chosen by closest distance to cluster centroid.
	Cluster representatives will be written to 1 traj (singlerep.nc), format Amber NetCDF
	Cluster representatives will be written to separate trajectories,
		prefix (rep), format PDB
	Average structures for clusters will be written to Avg, format Amber Restart
> run
Warning: One or more analyses requested creation of default COORDS DataSet.
    CREATECRD: Saving coordinates from Top ATGonium_dry13.prmtop to "_DEFAULTCRD_"
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES (1 total):
 0: ATGonium_dry13.prmtop, 103 atoms, 10 res, box: None, 1 mol

INPUT TRAJECTORIES (1 total):
 0: 'ATGonium_dry13.ann.traj' is an AMBER trajectory, Parm ATGonium_dry13.prmtop (reading 100 of 100)
  Coordinate processing will occur on 100 frames.

BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'ATGonium_dry13.prmtop' (1 actions):
  0: [createcrd _DEFAULTCRD_]
	Estimated memory usage (100 frames): 123.624 kB
----- ATGonium_dry13.ann.traj (1-100, 1) -----
 0% 10% 20% 30% 40% 51% 61% 71% 81% 91% 100% Complete.

Read 100 frames and processed 100 frames.
TIME: Avg. throughput= 3706.5866 frames / second.

ACTION OUTPUT:

ANALYSIS: Performing 1 analyses:
  0: [cluster C0 dbscan minpoints 25 epsilon 0.9 sievetoframe rms :1-10 sieve 10 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 restart]
	Starting clustering.
	Mask [:1-10] corresponds to 103 atoms.
	Estimated pair-wise matrix memory usage: > 0.244 kB
	Pair-wise matrix set up with sieve, 100 frames, 10 sieved frames.
	Calculating pair-wise distances.
 0% 11% 22% 33% 44% 56% 67% 78% 89% Complete.
	Memory used by pair-wise matrix and other cluster data: 0.732 kB
 0% 11% 22% 33% 44% 56% 67% 78% 89% 100% Complete.
	No clusters found.
	Cluster timing data:
TIME:	  Cluster Init. : 0.0000 s (  0.34%)
TIME:	  Pairwise Calc.: 0.0002 s ( 66.78%)
TIME:	  Clustering    : 0.0000 s (  7.80%)
TIME:	  Cluster Post. : 0.0000 s (  0.68%)
TIME:		Cluster renumbering/sieve restore 0.0000 s (  0.00%)
TIME:		Find best rep. 0.0000 s (  0.00%)
TIME:		Info calc 0.0000 s (  0.00%)
TIME:		Summary calc 0.0000 s (  0.00%)
TIME:		Coordinate writes 0.0000 s (  0.00%)
TIME:	Total: 0.0003 s

TIME: Analyses took 0.0004 seconds.

DATASETS (3 total):
	_DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 100 (123.624 kB) 103 atoms
	C0 "C0" (integer), size is 0
	C0[PWD] "C0[PWD]" (cluster matrix), size is 45

DATAFILES (2 total):
  cnumvtime.dat (Standard Data File):  C0
  cpopvtime.agr (Grace File): 
Warning: Set 'C0' contains no data.
Warning: File 'cnumvtime.dat' has no sets containing data.
Warning: File 'cpopvtime.agr' has no sets containing data.

RUN TIMING:
TIME:		Init               : 0.0001 s (  0.35%)
TIME:		Trajectory Process : 0.0270 s ( 97.35%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 0.0004 s (  1.27%)
TIME:		Data File Write    : 0.0000 s (  0.15%)
TIME:		Other              : 0.0002 s (  0.01%)
TIME:	Run Total 0.0277 s
---------- RUN END ---------------------------------------------------