CPPTRAJ: Trajectory Analysis. V16.00b OpenMP
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| Date/time: 06/02/16 12:26:47
| Available memory: 15.113 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 rms_1_2 :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 data rms_1_2 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 dataset rms_1_2
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 rms_1_2 :1-2&!@H= first mass]
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= 77.7239 frames / second.
ACTION OUTPUT:
ANALYSIS: Performing 1 analyses:
0: [cluster data rms_1_2 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.
Calculating pair-wise distances.
Random_Number: seed is <= 0, using wallclock time as seed (189050000)
Estimated pair-wise matrix memory usage: > 499.064 kB
Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames.
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: 42 points changed cluster assignment.
Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 2: 36 points changed cluster assignment.
Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 3: 13 points changed cluster assignment.
Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 4: 8 points changed cluster assignment.
Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 5: 4 points changed cluster assignment.
Round 6: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 6: 1 points changed cluster assignment.
Round 7: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 7: 1 points changed cluster assignment.
Round 8: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 8: 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 0.114415
#Cluster 1 has average-distance-to-centroid 0.151667
#Cluster 2 has average-distance-to-centroid 0.177764
#Cluster 3 has average-distance-to-centroid 0.191284
#Cluster 4 has average-distance-to-centroid 0.252506
#DBI: 0.511123
#pSF: 310026.255198
#Algorithm: Kmeans nclusters 5 maxit 100
#Representative frames: 17917 65484 63714 84570 17506
#Sieve value: 200 (random)
#Sieved frames: 144 512 766 892 1269 1353 1661 1715 1841 1859 2013 2065 2594 3098 4527 4893 4894 4968 4989 5345 5759 6112 6901 7264 7535 8514 8835 9000 9140 9147 9387 9467 9562 9573 9618 9782 9809 9995 10001 10015 10180 11260 11707 11730 11917 11933 12053 12779 12826 13272 13304 13420 13694 13807 14251 14289 14469 14651 14652 15013 15045 15196 15379 15491 15570 15741 15786 15904 15950 16012 16070 16155 16379 16410 16474 16652 16878 17084 17258 17438 17506 17529 17831 17917 17918 18232 18247 18261 18718 18878 19033 19141 19241 19348 19491 19537 19671 19681 20282 20378 20641 20690 20691 20952 21121 21143 21257 21378 21559 21662 22088 22135 22718 22792 23725 23826 23927 24025 24037 24505 24697 24791 24973 25166 25269 25297 25314 25596 26119 26245 26271 26504 26741 26743 27202 27207 27355 28049 28166 28167 28189 28225 28280 28408 28516 28559 28580 28660 28909 29013 29092 29198 29324 29339 29423 29424 29537 29553 29561 29629 29911 30065 30529 30795 30823 30860 30881 31176 31403 31791 31807 32092 32954 33613 33712 33753 33783 33863 33880 34146 34668 34854 34983 35228 35696 35748 35817 36435 37022 37250 37256 37431 37575 37885 37888 38388 38398 38556 38563 38629 38686 38884 38975 39072 39140 39311 39394 39543 39548 39770 39953 40452 40611 41100 41114 41209 41303 41489 41580 41844 42025 42238 42419 42476 42593 42930 43069 43392 43702 43735 43852 44028 44175 44334 44441 44525 44603 44679 44686 44786 45055 45256 45395 45454 45834 46958 47020 47100 47120 47147 47207 48352 48574 48983 49279 49384 49854 49970 50207 50248 50344 50549 50694 51842 52282 52450 52680 52791 52837 53049 53308 53802 53969 54167 54264 54431 54752 54832 55075 55517 55519 55547 55635 55692 55926 55961 56035 56287 56394 56555 56562 56745 56911 57006 57013 57016 57178 57313 57703 58058 58264 58539 58966 58997 59095 59177 59268 59436 59635 59666 59994 60379 60487 60643 61104 61281 61358 61373 61601 61664 62112 62155 62159 62190 62336 62535 62716 63055 63429 63504 63714 64100 64418 64471 65046 65163 65484 65738 66143 66483 66674 66719 66755 66960 66963 67027 67043 67214 67226 67334 67516 67541 67599 67776 67814 67973 68136 68164 68435 68689 69538 69772 70443 70461 70613 70625 70723 70753 70899 70900 71045 71243 71567 71781 72142 72376 72505 72596 73106 73299 73361 73408 73760 73826 74300 74924 75080 75148 75603 75636 76110 76147 76162 76644 77133 77140 78065 78071 78361 78450 78694 78949 79283 80331 80994 81078 81091 81235 81236 81390 81405 81822 81870 82093 82242 82535 82568 82730 82877 82973 83146 83219 83715 83844 83992 84028 84177 84570 84714 84952 85051 85219 85241 85258 85284 85288 85763 85985 86088 86195 86788 86789 87202 87646 87779 88004 88072 88250 88598 88905 88915 89002 89081 89514 89588 90159 90383 90495 90527 90743 91221 91731 92221 92472 92516 93016 93189 93227 93256 93576 93653 93753 93754 93956 94076 94260 94654 94695 94737 94822 96333 96440 96775 96888 96898 97130 97265 97771 97898 97906 97957 97966 97996 98320 98465 98952 99054 99598 99766 99966
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. : 0.3491 s ( 0.48%)
TIME: Pairwise Calc.: 0.0477 s ( 0.07%)
TIME: Clustering : 0.0049 s ( 0.01%)
TIME: Cluster Post. : 71.8350 s ( 99.44%)
TIME: Total: 72.2368 s
TIME: Analyses took 72.2368 seconds.
DATASETS (3 total):
rms_1_2 "rms_1_2" (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
RUN TIMING:
TIME: Init : 0.0000 s ( 0.00%)
TIME: Trajectory Process : 1286.6049 s ( 94.68%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 72.2368 s ( 5.32%)
TIME: Data File Write : 0.0001 s ( 0.00%)
TIME: Other : 0.0002 s ( 0.00%)
TIME: Run Total 1358.8420 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 1364.6282 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.