CPPTRAJ: Trajectory Analysis. V16.00b OpenMP
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| Date/time: 06/02/16 13:30:55
| Available memory: 15.679 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&!@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, 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= 70.8202 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 41 atoms.
Calculating pair-wise distances.
Random_Number: seed is <= 0, using wallclock time as seed (192100000)
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% 81% 91% 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: 11 points changed cluster assignment.
Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 4: 3 points changed cluster assignment.
Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 5: 1 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 0.866371
#Cluster 1 has average-distance-to-centroid 1.266668
#Cluster 2 has average-distance-to-centroid 1.111551
#Cluster 3 has average-distance-to-centroid 0.878301
#Cluster 4 has average-distance-to-centroid 1.824478
#DBI: 1.243015
#pSF: 35541.670881
#Algorithm: Kmeans nclusters 5 maxit 100
#Representative frames: 78009 87391 73000 57892 67964
#Sieve value: 200 (random)
#Sieved frames: 141 455 862 886 1031 1061 1936 1946 2184 2386 2401 2573 3029 3108 3236 3292 3317 3346 3347 3361 3740 3920 3926 4151 4263 4276 4392 4787 5013 5038 5561 6197 6341 6394 6410 6506 6509 6628 6648 6707 6934 6984 7082 7319 7509 7826 8189 8349 8363 8483 8827 8851 9214 9217 9912 10044 10451 10779 11515 11757 11781 11822 11929 12051 12070 12286 12480 12589 12665 12680 13073 13082 13177 13346 13409 13715 13740 13768 13928 14221 14255 14404 14441 14469 14569 14815 15119 15439 15468 15625 15646 15893 15919 15932 15982 16520 16712 16973 17049 17099 17365 17381 18022 18568 18670 18678 18692 19187 19313 19840 19874 19955 20155 20465 20474 21046 21230 21603 21698 21712 22254 22713 22883 23006 23345 23379 23582 23664 23743 23926 23997 24025 24087 24147 24577 24729 25688 25780 25915 26158 26287 26565 26596 26754 27132 27685 28257 28489 28694 29153 29308 29524 29938 30290 30355 30412 30643 30856 31040 31218 31259 31271 31281 31778 31847 32193 32226 32261 32300 32484 32508 32572 33002 33025 33126 33244 33380 33434 33583 34027 34331 34562 34998 35347 35692 35971 36315 36462 36487 36646 36939 37120 37485 37688 37690 37752 38019 38269 38301 38343 38777 39033 39341 39677 39774 39875 39879 39898 39938 40089 40158 40908 41022 41067 41769 42045 42191 42274 42347 42453 43649 43654 43748 43874 43889 44349 44770 44963 44984 45158 45477 45653 45680 45882 45897 46135 46196 46253 46657 47019 47131 47520 47731 47978 48011 48208 48252 48498 49056 49165 49238 49259 49507 49547 49879 50181 50377 50432 50501 51073 51263 51703 51832 51925 52120 52728 52745 52892 53093 53415 53561 53564 53736 53819 53993 54010 54721 55402 55427 55540 55733 55996 56059 56932 57144 57152 57367 57658 57702 57862 57892 57976 58008 58226 58330 58645 58740 58803 59167 59261 59551 59577 59752 59847 60119 60253 60272 60419 60444 60841 60960 61288 61399 61827 62247 62332 62460 62523 62586 62876 63216 63336 63402 63508 63696 64030 64088 64190 64590 64619 64999 65942 65991 66089 66188 66551 66788 66825 66915 67068 67262 67300 67415 67427 67617 67733 67964 68016 68181 68338 68458 68733 68781 69045 69167 69250 69457 69863 69976 70095 70251 70646 70760 70858 71595 71726 71835 72155 72192 72295 72533 72789 73000 73147 73459 73549 73660 73735 74087 74231 74499 74839 74850 75371 75732 76312 76323 76668 76670 76906 77432 77566 77834 78009 78129 78164 78188 78354 78397 78550 78955 78975 79184 79209 79666 79826 80004 80275 80323 80360 80543 80746 80853 81196 82199 82407 82510 82619 82867 83076 83166 83494 83913 83968 84006 84651 84755 84826 84920 85134 85198 85302 85378 85984 86177 86556 86568 86622 86985 87074 87391 87566 87582 87888 88460 88537 88610 88621 89531 89797 89895 90651 90798 90845 91045 91561 91844 91870 91944 92117 92124 93018 93164 93317 93498 93764 93949 94113 94380 94481 94625 94635 94703 95295 95312 95505 95676 95735 95863 96042 96664 96908 96968 97480 97602 97613 97796 97816 98235 98292 98396 98527 98694 98866 99018 99229 99260 99857 99955 99972
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. : 0.3630 s ( 0.50%)
TIME: Pairwise Calc.: 0.1528 s ( 0.21%)
TIME: Clustering : 0.0823 s ( 0.11%)
TIME: Cluster Post. : 72.0633 s ( 99.18%)
TIME: Total: 72.6614 s
TIME: Analyses took 72.6614 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 : 1412.0270 s ( 95.11%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 72.6614 s ( 4.89%)
TIME: Data File Write : 0.0000 s ( 0.00%)
TIME: Other : 0.0001 s ( 0.00%)
TIME: Run Total 1484.6886 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 1486.8785 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.