CPPTRAJ: Trajectory Analysis. V16.00b OpenMP
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| Date/time: 06/01/16 16:38:14
| Available memory: 15.996 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, 3300 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: 64 atoms, 2 res, box: Orthogonal, 1 mol
2: [rmsd :1-2&!@H= first mass out test.dat]
Target mask: [:1-2&!@H*](40)
Reference mask: [:1-2&!@H*](40)
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): 79.200 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= 88.5824 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 40 atoms.
Calculating pair-wise distances.
Random_Number: seed is <= 0, using wallclock time as seed (149540000)
Estimated pair-wise matrix memory usage: > 499.064 kB
Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames.
1% 11% 21% 31% 41% 50% 60% 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: 70 points changed cluster assignment.
Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 2: 9 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: No change. Skipping the rest of the iterations.
Restoring sieved frames.
Parallelizing calculation with 8 threads
0% 10% 20% 30% 40% 50% 60% 72% 84% 90% Complete.
#Clustering: 5 clusters 100000 frames
#Cluster 0 has average-distance-to-centroid 0.637680
#Cluster 1 has average-distance-to-centroid 0.979012
#Cluster 2 has average-distance-to-centroid 1.093808
#Cluster 3 has average-distance-to-centroid 1.709163
#Cluster 4 has average-distance-to-centroid 1.664395
#DBI: 1.111409
#pSF: 49296.639394
#Algorithm: Kmeans nclusters 5 maxit 100
#Representative frames: 25535 11879 68119 56967 95674
#Sieve value: 200 (random)
#Sieved frames: 59 89 90 1151 1322 1553 1607 1688 2035 2203 2226 2621 2729 2824 3054 3132 3449 3574 3989 4020 4398 4626 4812 4982 5015 5030 5054 5307 5768 5893 6037 6137 6300 6323 6345 6358 6384 6928 7189 7211 7536 7726 7945 8034 8053 8479 8730 8790 8842 8910 8914 8954 9152 9214 9607 9616 9880 9894 9935 10111 10245 10539 10637 10716 10753 10919 11048 11316 11879 12044 12133 12143 12265 12297 12298 12315 13031 13207 13386 13406 13942 14765 14785 14812 15149 15370 15377 15423 15480 15653 15848 15941 16098 16215 16873 16877 16889 16958 17178 17241 17524 17669 18289 18744 18751 19070 19206 19222 19327 19517 19639 19642 19930 20054 20112 20261 20611 20681 20790 20974 20996 21045 21223 21763 21767 21797 22225 22535 22596 22707 22756 23004 23614 23988 24407 24427 24475 24555 24811 24917 25265 25514 25535 25551 25682 25728 25842 26068 26125 26794 26903 27133 27391 27656 27943 28106 28355 28412 28566 28773 28892 28977 28994 29156 29241 29426 29521 29596 30037 30105 30391 30530 30540 30634 30704 30745 30827 30962 30987 31069 31233 31321 31410 31572 32756 33126 33517 33581 33817 33935 33969 34156 34234 34609 34698 34878 35323 35359 35453 35782 35906 36085 36250 36316 36724 37098 37110 37153 37187 37225 37327 37364 37432 37492 37714 37809 38050 38313 38341 38454 38570 38734 38752 38769 38829 38998 39152 39166 39529 39832 39963 40108 40377 40440 40973 41002 41011 41027 41114 41346 41501 42446 42658 42721 42899 42990 43942 43987 44155 44220 44325 44352 44480 45472 45917 46052 46203 46222 46303 46381 47364 47423 47464 47723 47764 47881 48058 48151 48312 48428 48508 48542 48669 48991 49251 49316 49734 50329 50341 50809 50899 50977 51172 51204 51213 51381 51844 52053 52191 52618 52645 52814 52980 53003 53145 53291 53542 53585 53643 53870 53973 53983 54122 54403 54715 54874 55300 55716 56281 56659 56967 57087 57180 57183 57282 57307 57552 57888 58515 58667 58689 58885 59000 59094 59986 60001 60414 61213 61263 61783 61840 63102 63283 63466 64031 64429 64582 64657 64715 65373 65468 65589 65680 66074 66089 66147 66258 66267 66484 66537 66615 66759 67025 67071 67183 67237 67521 67714 67911 68085 68119 68159 68171 68779 69065 69677 70768 70873 71025 71187 71712 71980 72051 72053 72059 72586 72590 72669 72995 73047 73209 73427 73656 74307 74487 74556 74654 74683 74705 74816 75054 75096 75192 75231 75644 76072 76190 76622 76803 77353 77749 78087 78105 78175 78407 78567 78981 78986 79330 79429 79648 80005 80112 80183 80302 80643 81099 81290 81379 81728 81888 82212 82286 82546 82682 82767 82781 82848 83139 83474 83546 84022 84223 84250 84460 84993 85116 85270 85273 85292 86233 86553 86738 86809 86936 86974 87135 87593 87654 87772 87825 88098 88407 88985 89141 89290 89509 89598 89714 89812 89985 90023 90083 90405 90452 90560 90713 90735 90752 90800 91701 92882 93539 93700 93823 93935 94138 94578 94590 94942 94972 95036 95291 95674 95710 95887 95978 96576 97085 97427 97596 97716 98001 98202 98509 99000 99361 99396 99766 99783
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. : 0.3099 s ( 0.52%)
TIME: Pairwise Calc.: 0.1008 s ( 0.17%)
TIME: Clustering : 0.0387 s ( 0.06%)
TIME: Cluster Post. : 59.1522 s ( 99.25%)
TIME: Total: 59.6017 s
TIME: Analyses took 59.6017 seconds.
DATASETS (3 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 100000
_DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 100000 (79.200 MB) Box Coords, 64 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 : 1128.8918 s ( 94.97%)
TIME: Action Post : 0.0207 s ( 0.00%)
TIME: Analysis : 59.6017 s ( 5.01%)
TIME: Data File Write : 0.1337 s ( 0.01%)
TIME: Other : 0.0001 s ( 0.00%)
TIME: Run Total 1188.6480 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 1193.6468 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.