CPPTRAJ: Trajectory Analysis. V16.00b OpenMP
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| Date/time: 06/01/16 18:40:25
| Available memory: 16.035 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]
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@C5',C4',C3',O3',P,C2 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@C5',C4',C3',O3',P,C2]) 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, 3301 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: 65 atoms, 2 res, box: Orthogonal, 1 mol
2: [rmsd :1-2&!@H= first mass]
Target mask: [:1-2&!@H*](41)
Reference mask: [:1-2&!@H*](41)
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): 80.400 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= 87.0678 frames / second.
ACTION OUTPUT:
ANALYSIS: Performing 1 analyses:
0: [cluster :1,2@C5',C4',C3',O3',P,C2 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@C5',C4',C3',O3',P,C2] corresponds to 11 atoms.
Calculating pair-wise distances.
Random_Number: seed is <= 0, using wallclock time as seed (151000000)
Estimated pair-wise matrix memory usage: > 499.064 kB
Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames.
1% 10% 21% 31% 41% 51% 61% 71% 80% 90% 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: 56 points changed cluster assignment.
Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 2: 30 points changed cluster assignment.
Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 3: 18 points changed cluster assignment.
Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 4: 13 points changed cluster assignment.
Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 5: 3 points changed cluster assignment.
Round 6: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 6: 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 0.649766
#Cluster 1 has average-distance-to-centroid 0.894613
#Cluster 2 has average-distance-to-centroid 0.888360
#Cluster 3 has average-distance-to-centroid 0.852834
#Cluster 4 has average-distance-to-centroid 1.429668
#DBI: 1.177027
#pSF: 43087.373443
#Algorithm: Kmeans nclusters 5 maxit 100
#Representative frames: 8291 24264 65896 64985 46609
#Sieve value: 200 (random)
#Sieved frames: 110 456 488 513 606 663 851 1011 1331 1580 1613 1633 2394 2859 2866 2973 2987 3102 3393 3598 3735 4045 4762 4778 5012 5013 5290 5360 5651 6117 6226 6574 6734 7502 7658 7685 7989 8291 8340 8357 8520 9043 9214 9280 9284 9644 10080 10147 10922 11077 11170 11248 11750 11835 11846 12059 12230 12354 12431 12438 12487 12584 12719 12785 12963 13112 13180 13419 13608 14084 14102 14126 14519 14908 15038 15238 15756 16968 17073 17212 17474 17674 17852 18383 18689 18759 18778 19074 19158 19415 19607 19767 19801 19920 20081 20094 20136 20288 20464 20528 20651 21275 21666 21901 22081 22194 22264 22429 22822 22915 23012 23091 23193 24244 24264 24383 24443 25014 25089 25225 25334 25336 25642 25711 25712 25871 26011 26203 26589 26664 26674 26963 27012 27118 27233 27239 27284 27593 27633 27874 27929 28120 28408 28538 28787 28849 29233 29247 29254 29280 29776 29787 29834 30422 30889 30952 31218 31397 31508 31567 31716 31786 31820 31843 31905 32049 32140 32308 32429 32885 33092 33106 33291 33743 33828 34048 34165 34380 34468 34492 34777 34933 35030 35074 35311 35375 35611 35673 35742 36129 37022 37324 37625 37720 37747 37935 37938 38215 38359 38504 39356 39392 39406 39867 40019 40595 41090 41196 41209 41352 42051 42166 42515 42519 42561 42688 42789 42966 43276 44016 44404 44435 44889 44979 45420 45554 45614 45772 46036 46237 46421 46609 46847 46882 46890 46931 47404 47479 47818 47886 48036 48222 48453 48799 48825 48984 49014 49169 49205 49614 49779 49818 49946 50262 50408 50644 50845 50956 51218 51274 51356 51551 51645 51710 52612 52657 52740 53246 53326 53344 53578 53804 53863 53936 54360 54541 55109 55143 55328 55334 56701 56875 56893 57030 57118 57266 57405 57560 57682 57857 58422 58476 58523 58710 58819 58825 59154 59161 59283 59543 59628 60182 60203 60483 60861 61013 61329 61419 61428 61446 61456 61836 61913 62076 62119 62183 62483 62623 62677 62811 62813 62897 62981 63226 63690 63802 63881 64322 64390 64439 64462 64713 64949 64985 65004 65377 65827 65848 65896 65985 66792 66909 67295 67423 67690 68542 68663 69127 69218 69281 69384 69901 69936 70000 70060 70288 70362 70563 70586 70736 71124 71839 72668 72791 72882 72888 73146 73499 73634 73731 73845 73881 73957 73968 74019 74152 74396 75175 75325 75646 75683 75969 76050 76281 76418 76432 76868 77087 77481 77562 77651 77701 78327 78739 78844 78847 79000 79152 79275 79497 79501 79714 79773 80068 80909 81149 81252 81287 81633 81950 81959 82350 82685 82943 83271 83331 84300 84578 84591 84638 84904 84972 85628 85956 86151 86329 86471 86579 86864 86903 87134 87229 87586 87628 87817 87849 87946 88277 88322 88534 88538 88578 88661 88782 89080 89590 89734 89880 90322 90382 90700 90817 90958 91110 91374 91418 91421 91626 92126 92208 92570 92968 93231 93386 93636 93802 93961 94227 94413 94451 94626 94805 94862 95251 95680 95844 95923 95974 95978 96089 96223 96344 96527 96601 96652 96661 96799 96878 97085 97250 98511 98549 98645 98672 99005 99017 99327 99505 99968 99992
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. : 0.3340 s ( 0.56%)
TIME: Pairwise Calc.: 0.0615 s ( 0.10%)
TIME: Clustering : 0.0371 s ( 0.06%)
TIME: Cluster Post. : 58.9563 s ( 99.27%)
TIME: Total: 59.3890 s
TIME: Analyses took 59.3890 seconds.
DATASETS (3 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 100000
_DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 100000 (80.400 MB) Box Coords, 65 atoms
Cnum_00003 "Cnum_00003" (integer), size is 100000
RUN TIMING:
TIME: Init : 0.0000 s ( 0.00%)
TIME: Trajectory Process : 1148.5305 s ( 95.08%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 59.3890 s ( 4.92%)
TIME: Data File Write : 0.0000 s ( 0.00%)
TIME: Other : 0.0003 s ( 0.00%)
TIME: Run Total 1207.9199 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 1208.7563 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.