CPPTRAJ: Trajectory Analysis. V16.00b OpenMP
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| Date/time: 06/02/16 12:57:12
| Available memory: 15.841 GB
INPUT: Reading input from 'pt-clust.in'
[parm ../../tip3p/ff12sb/run1/build/full.topo.hmr [tip3p-ff12sb]]
Reading '../../tip3p/ff12sb/run1/build/full.topo.hmr' as Amber Topology
[trajin ../../tip3p/ff12sb/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/ff12sb/run1/traj.1.02,../../tip3p/ff12sb/run1/traj.1.03,../../tip3p/ff12sb/run1/traj.1.04,../../tip3p/ff12sb/run1/traj.1.05,../../tip3p/ff12sb/run1/traj.1.06,../../tip3p/ff12sb/run1/traj.1.07,../../tip3p/ff12sb/run1/traj.1.08,../../tip3p/ff12sb/run1/traj.1.09,../../tip3p/ff12sb/run1/traj.1.10,../../tip3p/ff12sb/run1/traj.1.11,../../tip3p/ff12sb/run1/traj.1.12,../../tip3p/ff12sb/run1/traj.1.13,../../tip3p/ff12sb/run1/traj.1.14,../../tip3p/ff12sb/run1/traj.1.15,../../tip3p/ff12sb/run1/traj.1.16,../../tip3p/ff12sb/run1/traj.1.17,../../tip3p/ff12sb/run1/traj.1.18 parm [tip3p-ff12sb]]
Reading '../../tip3p/ff12sb/run1/traj.1.01' as Amber NetCDF
[trajin ../../tip3p/ff12sb/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/ff12sb/run2/traj.1.02,../../tip3p/ff12sb/run2/traj.1.03,../../tip3p/ff12sb/run2/traj.1.04,../../tip3p/ff12sb/run2/traj.1.05,../../tip3p/ff12sb/run2/traj.1.06,../../tip3p/ff12sb/run2/traj.1.07,../../tip3p/ff12sb/run2/traj.1.08,../../tip3p/ff12sb/run2/traj.1.09,../../tip3p/ff12sb/run2/traj.1.10,../../tip3p/ff12sb/run2/traj.1.11,../../tip3p/ff12sb/run2/traj.1.12,../../tip3p/ff12sb/run2/traj.1.13,../../tip3p/ff12sb/run2/traj.1.14,../../tip3p/ff12sb/run2/traj.1.15,../../tip3p/ff12sb/run2/traj.1.16,../../tip3p/ff12sb/run2/traj.1.17,../../tip3p/ff12sb/run2/traj.1.18 parm [tip3p-ff12sb]]
Reading '../../tip3p/ff12sb/run2/traj.1.01' as Amber NetCDF
[autoimage origin]
AUTOIMAGE: To origin based on center of mass, anchor is first molecule.
[strip :WAT,Na+,Cl-]
STRIP: Stripping atoms in mask [:WAT,Na+,Cl-]
[rmsd :1-2&!@H= first mass out test.dat]
RMSD: (:1-2&!@H*), reference is first frame (:1-2&!@H*), mass-weighted.
Best-fit RMSD will be calculated, coords will be rotated and translated.
[cluster :1,2&!@H= summary clust-summary.dat repout rep repfmt pdb clusterout ctraj clusterfmt netcdf kmeans clusters 5 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000]
CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask [:1,2&!@H=]) best-fit
K-MEANS: Looking for 5 clusters.
Sequentially modify each point.
Cluster to cluster distance will be based on cluster centroids.
Initial clustering will be randomly sieved (with value 200).
Previously calcd pair distances CpptrajPairDist will be used if found.
Summary of cluster results will be written to clust-summary.dat
Summary comparing parts of trajectory data for clusters will be written to split.dat
Frames will be split at: 50000 100000
Cluster trajectories will be written to ctraj, format Amber NetCDF
Cluster representatives will be written to separate trajectories,
prefix (rep), format PDB
Warning: One or more analyses requested creation of default COORDS DataSet.
CREATECRD: Saving coordinates from Top full.topo.hmr to "_DEFAULTCRD_"
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: [tip3p-ff12sb] full.topo.hmr, 3298 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent
INPUT TRAJECTORIES (2 total):
0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000)
Looking for frames at 298.41 K
1: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000)
Looking for frames at 298.41 K
Coordinate processing will occur on 100000 frames.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'full.topo.hmr' (4 actions):
0: [autoimage origin]
Anchor molecule is 1
1086 molecules are mobile.
1: [strip :WAT,Na+,Cl-]
Stripping 3236 atoms.
Stripped topology: 62 atoms, 2 res, box: Orthogonal, 1 mol
2: [rmsd :1-2&!@H= first mass out test.dat]
Target mask: [:1-2&!@H*](39)
Reference mask: [:1-2&!@H*](39)
Warning: Coordinates are being rotated and box coordinates are present.
Warning: Unit cell vectors are NOT rotated; imaging will not be possible
Warning: after the RMS-fit is performed.
3: [createcrd _DEFAULTCRD_]
Warning: COORDS data sets do not store temperatures.
Warning: COORDS data sets do not store times.
Estimated memory usage (100000 frames): 76.800 MB
----- traj.1.01 (1-50000, 1) -----
0% 10% 20% 30% 40%
----- traj.1.01 (1-50000, 1) -----
50% 60% 70% 80% 90% 100% Complete.
Read 100000 frames and processed 100000 frames.
TIME: Avg. throughput= 80.2802 frames / second.
ACTION OUTPUT:
ANALYSIS: Performing 1 analyses:
0: [cluster :1,2&!@H= summary clust-summary.dat repout rep repfmt pdb clusterout ctraj clusterfmt netcdf kmeans clusters 5 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000]
Starting clustering.
Mask [:1,2&!@H*] corresponds to 39 atoms.
Calculating pair-wise distances.
Random_Number: seed is <= 0, using wallclock time as seed (190540000)
Estimated pair-wise matrix memory usage: > 499.064 kB
Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames.
0% 10% 21% 31% 41% 51% 61% 71% 81% 92% Complete.
Saving pair-wise distances to CpptrajPairDist
Memory used by pair-wise matrix and other cluster data: 999.160 kB
Round 0: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 0: 495 points changed cluster assignment.
Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 1: 31 points changed cluster assignment.
Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 2: 10 points changed cluster assignment.
Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 3: 3 points changed cluster assignment.
Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 4: 1 points changed cluster assignment.
Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 5: No change. Skipping the rest of the iterations.
Restoring sieved frames.
Parallelizing calculation with 8 threads
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Complete.
#Clustering: 5 clusters 100000 frames
#Cluster 0 has average-distance-to-centroid 1.221110
#Cluster 1 has average-distance-to-centroid 1.420650
#Cluster 2 has average-distance-to-centroid 1.564955
#Cluster 3 has average-distance-to-centroid 1.511873
#Cluster 4 has average-distance-to-centroid 1.699063
#DBI: 1.466157
#pSF: 14451.924966
#Algorithm: Kmeans nclusters 5 maxit 100
#Representative frames: 45706 80162 25825 9449 11150
#Sieve value: 200 (random)
#Sieved frames: 895 1049 1088 1155 1163 1287 1423 1469 1882 2039 2287 2804 3558 3740 3793 3859 3882 4115 4806 5160 5694 5865 6116 6915 7150 7437 7491 7654 7775 7961 8069 8233 8321 8443 8790 9120 9449 9797 9939 10497 10666 10978 10980 11150 11181 11486 11808 11954 12073 12892 13016 13139 13403 13901 13933 14034 14102 14209 14452 14539 14563 14788 14795 14867 14930 14981 14985 15541 15632 15637 16163 16215 16252 16389 16410 16469 16751 16870 17141 17799 17915 18005 18479 18637 18642 19039 19971 20018 20045 20110 20246 20368 20394 20421 20446 20505 20858 20877 20890 20936 22376 22574 22894 22984 23072 23214 23615 23631 24014 24502 24607 24623 25625 25664 25717 25825 25887 25907 25918 26219 26227 26466 26635 26690 26812 27007 27109 27277 27281 27350 27778 27917 28050 28154 28161 28332 28357 28765 28809 28908 29136 29903 29968 30148 30244 30563 30612 30736 31107 31555 31601 31745 31859 31970 32013 32085 32163 32397 32637 32662 32825 32833 32935 32980 33422 33483 33604 33790 34643 34858 34864 34898 35011 35106 35202 35495 35595 35942 36139 36574 36895 36985 37065 37100 37112 37675 37919 38061 38583 38674 38956 39042 39099 39385 39813 39842 39923 39949 40201 40238 40430 40479 40483 40638 41090 41114 41496 42034 42180 42202 42328 43003 43026 43088 43173 43289 43418 43546 43564 44399 44488 44653 44845 44915 45149 45570 45591 45617 45630 45706 46031 46225 46339 46377 46494 46682 46737 46962 47126 47184 47288 47361 47372 47401 47460 47757 47782 47856 48066 48527 48615 49117 49199 49228 49288 49663 49907 49979 50091 50096 50171 50253 50527 50567 50816 50919 51059 51062 51237 51785 51850 51986 51994 52182 52184 52371 52439 52606 52620 52858 52900 52936 53107 53214 53261 53498 53674 53758 54072 54824 54919 55095 55203 55318 55331 55432 55444 55663 55672 56408 56477 56809 57156 57192 57441 57510 57737 58638 58793 59054 59115 59272 59540 60513 60677 60987 61022 61026 61099 61319 61661 62195 62262 62270 62466 62608 63038 63603 63797 63900 64617 64783 64993 65009 65895 66466 66480 66485 66829 66834 67066 67117 67165 67334 67763 67787 68023 68725 68777 68900 69216 69245 69396 69855 69994 70070 70138 70297 70720 71028 71083 71318 71516 71647 71705 71949 71960 72101 72232 72285 72380 72563 72668 72941 73130 73173 73299 73520 73559 73717 73919 73963 73967 73992 74206 74391 74439 74806 75111 75117 75421 75539 75932 75938 76079 76084 76132 76282 76330 76705 76785 77082 77166 77525 77693 78122 78324 78656 79565 79568 79776 79977 80162 80177 80349 80540 80717 80749 81362 81407 81969 81985 82307 82545 82816 82889 83112 83724 83870 83879 83989 83990 84026 84636 84945 84950 85064 85156 85525 85704 85840 85965 86484 86527 86754 86778 86984 87038 87182 87287 87722 87766 87842 88280 88282 88313 88334 88817 88915 89445 89486 89961 90327 90525 90630 90911 90994 91645 93063 93257 93337 93447 93643 93827 94540 94720 95179 95228 95293 95297 95359 95453 95813 96062 96115 96435 97216 97294 97353 97510 97874 98054 98349 98609 98625 98686 98827 98979 98991 99732
Warning: split frame 100000 is out of bounds; ignoring.
Writing 'ctraj.c0' as Amber NetCDF
Writing 'ctraj.c1' as Amber NetCDF
Writing 'ctraj.c2' as Amber NetCDF
Writing 'ctraj.c3' as Amber NetCDF
Writing 'ctraj.c4' as Amber NetCDF
Writing 'rep.c0.pdb' as PDB
Warning: No PDB space group specified.
Writing 'rep.c1.pdb' as PDB
Warning: No PDB space group specified.
Writing 'rep.c2.pdb' as PDB
Warning: No PDB space group specified.
Writing 'rep.c3.pdb' as PDB
Warning: No PDB space group specified.
Writing 'rep.c4.pdb' as PDB
Warning: No PDB space group specified.
Cluster timing data:
TIME: Cluster Init. : 0.3070 s ( 0.42%)
TIME: Pairwise Calc.: 0.0934 s ( 0.13%)
TIME: Clustering : 0.1146 s ( 0.16%)
TIME: Cluster Post. : 72.7935 s ( 99.30%)
TIME: Total: 73.3085 s
TIME: Analyses took 73.3085 seconds.
DATASETS (3 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 100000
_DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 100000 (76.800 MB) Box Coords, 62 atoms
Cnum_00003 "Cnum_00003" (integer), size is 100000
DATAFILES (1 total):
test.dat (Standard Data File): RMSD_00001
RUN TIMING:
TIME: Init : 0.0000 s ( 0.00%)
TIME: Trajectory Process : 1245.6370 s ( 94.43%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 73.3085 s ( 5.56%)
TIME: Data File Write : 0.1653 s ( 0.01%)
TIME: Other : 0.0001 s ( 0.00%)
TIME: Run Total 1319.1110 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 1321.0101 seconds.
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To cite CPPTRAJ use:
Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
Theory Comput., 2013, 9 (7), pp 3084-3095.