CPPTRAJ: Trajectory Analysis. V16.00b OpenMP
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| Date/time: 05/25/16 15:38:06
| Available memory: 16.030 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 7 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 7 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= 25.9363 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 7 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 (149030000)
Estimated pair-wise matrix memory usage: > 499.064 kB
Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames.
0% 10% 20% 30% 40% 51% 61% 71% 81% 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: 493 points changed cluster assignment.
Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 1: 21 points changed cluster assignment.
Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 2: 1 points changed cluster assignment.
Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 3: 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: 7 clusters 100000 frames
#Cluster 0 has average-distance-to-centroid 0.687008
#Cluster 1 has average-distance-to-centroid 1.245878
#Cluster 2 has average-distance-to-centroid 1.416083
#Cluster 3 has average-distance-to-centroid 1.581430
#Cluster 4 has average-distance-to-centroid 1.543858
#Cluster 5 has average-distance-to-centroid 1.588568
#Cluster 6 has average-distance-to-centroid 1.585511
#DBI: 1.589850
#pSF: 25246.297466
#Algorithm: Kmeans nclusters 7 maxit 100
#Representative frames: 60483 66617 22942 66675 89267 64320 56699
#Sieve value: 200 (random)
#Sieved frames: 135 319 351 502 786 851 857 981 2258 3357 3595 3612 4102 4216 4462 4606 4685 4924 5151 5202 5319 5374 5697 5784 6049 6100 6138 6496 6623 6763 6766 7637 7659 8066 8106 8231 8352 8490 8531 8614 8699 8941 9083 9170 9185 9189 9219 9222 9779 9918 9935 10272 10532 10750 10839 10907 11031 11156 11183 11262 11414 11428 11581 11787 11967 12018 12038 12337 12713 12728 12862 13174 13315 13355 13360 13519 13692 13725 13884 13904 13989 14023 14212 14692 14823 14863 14986 15043 15190 15444 15576 16212 16344 16454 17111 17190 17274 17312 17375 17850 18516 18584 18643 18693 18988 19386 19503 19533 19801 19865 20061 20076 20078 20429 21189 21289 21390 21502 21680 21974 22154 22218 22253 22481 22644 22809 22942 23190 24046 24132 24143 24515 24592 24677 25009 25126 25253 25255 25303 25363 25626 25647 26308 26374 26840 27077 27196 27382 27815 28033 29095 29242 29378 29631 29804 29871 30217 30376 30440 30634 30674 30909 30925 30930 31457 31578 31598 32079 32381 32680 32706 32862 33222 33725 34056 34235 34502 34524 34573 34887 34919 34986 35092 35142 35792 35852 35992 36037 36062 36235 36921 37146 37189 37248 37948 38019 38044 38209 38493 38726 38730 38938 38958 39153 39240 39272 39419 39559 39890 40075 40274 40277 40282 40384 40472 40480 40925 41026 41037 41229 41233 41266 41320 41916 41958 42127 42440 42496 42542 42563 42605 42914 42972 43172 43299 43448 43699 44033 44375 44722 44847 44863 45380 45549 45554 45696 46000 46166 46503 46923 47026 47188 47370 47489 47666 47968 48008 48440 48528 48789 49610 49724 49730 50134 50379 50755 50976 51037 51134 51154 51699 51701 51705 52040 52158 52436 52623 52646 52905 53055 53226 53640 53843 54026 54214 54555 54680 54841 54923 54989 55438 55568 55575 55892 56017 56019 56601 56618 56699 56768 56959 57174 58267 58466 58477 58504 58506 58538 58563 58912 59167 59226 59273 59363 59837 60483 60544 60555 60804 61229 61394 61579 61700 61723 61736 62070 62804 62854 63014 63120 63778 63835 64142 64320 64886 64906 65140 65156 65420 65468 65496 65522 66101 66251 66308 66617 66656 66675 66754 66922 66990 67000 67051 67095 67518 67660 68055 68088 68561 68852 68999 69517 70445 70558 70821 70912 71126 71301 71456 71530 72235 72467 72495 72517 72697 72884 72985 73551 73637 73704 73841 74189 74228 74300 74514 74695 74768 74942 75150 75580 76544 76609 76707 76716 76915 77016 77251 77298 77652 77724 77774 77802 78125 78247 78350 78537 78715 79259 79438 79461 79530 79638 79942 80009 80205 80384 80588 80657 80701 80768 81038 81651 82161 82525 83063 83164 83302 83598 83603 84042 84167 84307 84921 84951 84999 85594 85723 85967 86215 86231 86532 86566 86589 86951 87070 87850 88268 88589 89069 89267 89325 89643 89699 90002 90575 90778 90863 90923 91290 91371 91730 93055 93199 93283 93589 93885 94022 94130 94548 94637 94771 95313 95498 95505 95521 95726 95892 96210 96469 96619 96748 96971 97053 97452 97542 97583 97622 97633 98285 98393 98819 98865 98999 99130 99194 99421 99726 99852 99877 99988
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 'ctraj.c5' as Amber NetCDF
Writing 'ctraj.c6' 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.
Writing 'rep.c5.pdb' as PDB
Warning: No PDB space group specified.
Writing 'rep.c6.pdb' as PDB
Warning: No PDB space group specified.
Cluster timing data:
TIME: Cluster Init. : 0.3276 s ( 0.56%)
TIME: Pairwise Calc.: 0.1025 s ( 0.17%)
TIME: Clustering : 0.0387 s ( 0.07%)
TIME: Cluster Post. : 58.3261 s ( 99.20%)
TIME: Total: 58.7949 s
TIME: Analyses took 58.7949 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 : 3855.5983 s ( 98.49%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 58.7949 s ( 1.50%)
TIME: Data File Write : 0.1374 s ( 0.00%)
TIME: Other : 0.0001 s ( 0.00%)
TIME: Run Total 3914.5308 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 3916.4367 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.