CPPTRAJ: Trajectory Analysis. V16.00b OpenMP
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| Date/time: 06/02/16 13:31:54
| Available memory: 16.009 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, 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 rms_1_2 :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= 70.6981 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 (189700000)
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: 15 points changed cluster assignment.
Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 2: 17 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: 11 points changed cluster assignment.
Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 5: 20 points changed cluster assignment.
Round 6: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 6: 26 points changed cluster assignment.
Round 7: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 7: 18 points changed cluster assignment.
Round 8: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 8: 15 points changed cluster assignment.
Round 9: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 9: 20 points changed cluster assignment.
Round 10: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 10: 12 points changed cluster assignment.
Round 11: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 11: 4 points changed cluster assignment.
Round 12: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 12: 8 points changed cluster assignment.
Round 13: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 13: 10 points changed cluster assignment.
Round 14: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 14: 5 points changed cluster assignment.
Round 15: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 15: 3 points changed cluster assignment.
Round 16: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 16: 3 points changed cluster assignment.
Round 17: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 17: 2 points changed cluster assignment.
Round 18: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 18: 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 0.116129
#Cluster 1 has average-distance-to-centroid 0.118802
#Cluster 2 has average-distance-to-centroid 0.114133
#Cluster 3 has average-distance-to-centroid 0.120337
#Cluster 4 has average-distance-to-centroid 0.153402
#DBI: 0.499395
#pSF: 545761.245180
#Algorithm: Kmeans nclusters 5 maxit 100
#Representative frames: 87527 53048 9521 43178 18062
#Sieve value: 200 (random)
#Sieved frames: 30 93 162 169 482 745 846 944 982 1395 2276 2351 2519 2699 2797 2971 3123 3409 3477 3613 4104 4573 4822 4959 5299 5372 5591 5949 6356 6807 7109 7169 7372 7620 7850 7934 8134 8239 8540 8730 8887 9063 9278 9305 9521 9782 10013 10166 11012 11040 11319 11386 11644 11875 11877 11932 12220 12222 12338 12569 12840 12897 13130 13320 13497 13661 13828 14137 14208 14399 14493 14527 14549 14683 15055 15257 15553 15872 16022 16162 16204 16730 17022 17285 17681 17810 17844 17886 17940 17965 17968 18062 18315 18450 18868 18923 19892 19895 20026 20163 20192 20334 20452 20558 20752 20948 21100 21295 21391 21599 21725 21818 22019 22030 22087 22148 22329 22617 23127 23219 23293 23621 23793 23922 24432 24512 25214 25556 26126 26200 26217 26281 26814 26922 27417 28043 28370 29077 29109 29178 29236 29525 29650 29678 30029 30152 30795 31237 31480 31531 31571 32018 32345 32751 32847 32873 33325 33328 33802 34057 34231 35587 35611 35782 35911 36264 36303 36327 36576 36709 36759 36769 36797 37229 37234 37412 37415 37454 38101 38211 39108 39515 39684 39711 39737 39913 40100 40151 40698 40769 40983 41076 41146 41197 41297 41375 41833 41944 42083 42121 42224 42551 42606 42661 42715 42915 42994 43018 43141 43170 43178 43342 43432 43534 44065 44434 44896 45270 45332 45527 45734 45849 45903 46275 46404 46460 46834 47303 47499 47596 47896 47943 48347 48392 48487 48511 48596 48850 48936 49045 49185 49590 49746 49925 50015 50445 50865 50905 51111 51585 51607 51676 51689 51709 52062 52265 52485 52610 52867 52931 53048 53279 53374 53697 53741 53771 53893 54008 54369 54378 54510 54563 54691 54848 54856 55088 55211 55274 55386 55407 55615 55773 55845 55888 55917 56499 56511 56830 56996 57355 57415 57903 58049 58050 58517 58596 58641 58647 59498 59710 59897 60096 60283 60412 60712 60856 60868 60995 61408 61432 61626 61757 62172 62590 63112 63118 63183 63430 63625 64052 64073 64685 64813 64880 65023 65059 65338 65402 65968 66241 66442 66896 67237 67364 67535 67664 67674 67823 68114 68387 69058 69739 69877 69942 70065 70409 70429 70481 70725 70925 71103 71343 71618 71652 71829 71853 72039 72080 72283 72338 72559 72627 72706 72869 73072 73203 73347 73687 73807 73938 74009 74320 74472 74563 74744 74862 75057 75080 75794 75880 76165 76170 76328 76351 76709 76769 76818 77652 77662 77747 78005 78179 79171 79340 79878 79886 80048 80297 81152 81462 81922 82204 82641 82899 83401 83447 83927 84159 84168 84235 84254 84413 84445 84462 84801 84856 85189 85341 85939 86034 86214 86250 86301 86403 86671 86677 86733 86987 87173 87267 87527 87531 87550 87572 87766 87914 88212 88251 88271 88355 88700 88803 88830 89479 89786 90011 90194 90245 90670 90855 91448 91706 92023 92096 92549 92660 92962 93458 93606 93663 94015 94022 94197 94299 94497 94536 94605 94695 94714 94894 95127 95199 95206 95212 95214 95630 96073 96091 96095 96829 96967 96984 97035 97347 97349 97754 97991 98047 98204 98440 98547 98643 98693 98835 98884 99104 99390 99549 99630 99703
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. : 0.3463 s ( 0.48%)
TIME: Pairwise Calc.: 0.0701 s ( 0.10%)
TIME: Clustering : 0.0078 s ( 0.01%)
TIME: Cluster Post. : 71.1556 s ( 99.41%)
TIME: Total: 71.5797 s
TIME: Analyses took 71.5798 seconds.
DATASETS (3 total):
rms_1_2 "rms_1_2" (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 : 1414.4645 s ( 95.18%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 71.5798 s ( 4.82%)
TIME: Data File Write : 0.0001 s ( 0.00%)
TIME: Other : 0.0005 s ( 0.00%)
TIME: Run Total 1486.0449 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 1486.9396 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.