CPPTRAJ: Trajectory Analysis. V16.00b OpenMP
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 05/29/16 22:45:37
| Available memory: 16.143 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 6 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 6 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, 3299 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: 63 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): 78.000 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= 87.3196 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 6 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 (151790000)
Estimated pair-wise matrix memory usage: > 499.064 kB
Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames.
0% 10% 21% 30% 40% 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: 494 points changed cluster assignment.
Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 1: 43 points changed cluster assignment.
Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 2: 23 points changed cluster assignment.
Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 3: 9 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% 70% 80% 90% Complete.
#Clustering: 6 clusters 100000 frames
#Cluster 0 has average-distance-to-centroid 0.979686
#Cluster 1 has average-distance-to-centroid 1.222100
#Cluster 2 has average-distance-to-centroid 1.222530
#Cluster 3 has average-distance-to-centroid 1.271139
#Cluster 4 has average-distance-to-centroid 1.884020
#Cluster 5 has average-distance-to-centroid 1.667470
#DBI: 1.721270
#pSF: 20619.173990
#Algorithm: Kmeans nclusters 6 maxit 100
#Representative frames: 14824 26604 50613 3975 3002 57635
#Sieve value: 200 (random)
#Sieved frames: 45 70 525 626 721 986 1549 1830 1842 1877 2466 2662 2895 3002 3930 3961 3975 4043 4093 4117 4155 4517 4707 4748 4835 4980 5132 5135 5213 5214 5328 5341 5542 5697 5798 5981 5993 6105 6291 6348 6381 6705 6763 6893 7770 7821 7858 8073 8203 8471 8553 8823 8955 9040 9328 9336 9399 9687 9860 9864 9927 10245 10548 10549 10565 10652 10812 11201 11400 11440 11471 11751 11797 11828 12130 12621 12714 12787 13124 13437 13877 14110 14121 14359 14475 14540 14673 14824 15393 15464 15488 15503 15716 16032 17010 17474 17542 17951 17989 18208 18366 18656 19030 19417 19758 20444 20500 20884 20966 21286 21324 21455 21581 21655 21906 22035 22061 22267 22272 22320 22449 22634 22757 22972 23103 23252 23925 24300 24310 24449 24788 24974 25190 25305 25628 25631 26042 26057 26604 27089 27128 27376 27384 27537 27898 27989 28025 28375 28463 28760 28816 29103 29258 29377 29417 29535 29551 29612 29810 29909 29932 30642 31468 31563 31851 31890 32117 32143 32333 32470 32917 33119 33334 33374 33753 33791 34189 34252 34504 34578 34694 34711 34867 34886 34890 35081 35782 36603 37146 37443 37529 37583 37740 38057 38283 38438 38506 38679 38685 38877 39079 39201 39276 39513 39949 40189 40270 40296 40578 40582 40629 40650 40740 40890 40964 41332 41484 41567 41993 42002 42112 42193 42264 42830 42920 43086 43440 43592 43938 43988 44400 44680 44693 44855 45040 45092 45131 45224 46226 46310 46692 46729 46919 47014 47396 47544 47809 48238 48605 48645 48709 48822 49316 49485 49512 49651 49683 49759 49783 50300 50613 50834 51041 51091 51368 51925 52246 52636 52765 52801 52881 53157 53597 53643 53833 54521 54571 54771 54781 54803 54963 55137 55161 55391 55443 55910 55926 56049 56259 56790 57499 57635 58749 59279 59535 59851 59873 59894 59933 60189 60564 60811 60883 60952 61007 61477 62325 62370 62418 62581 62582 62772 62946 63016 63087 63456 63895 64224 64279 64716 64768 64863 65073 65377 65849 66145 66197 66605 67255 67932 68161 68243 68463 68492 68494 68592 68636 68856 68924 68943 69109 69189 69357 69583 69597 69697 69704 69708 69829 69871 70084 70411 70650 70686 70845 70942 71214 71351 71457 71819 71831 72009 72057 72501 73236 73678 73950 74254 74623 74762 74764 74833 74847 74896 74993 75210 75355 75411 75663 76137 76417 76474 76719 76762 77360 77609 77811 77816 77863 77889 78168 78312 78362 78596 78613 78784 79005 79047 79113 79252 79282 79561 79700 80032 80443 80446 80851 82000 82506 82563 82627 82634 82740 83016 83051 83276 83337 83765 84669 84915 85085 85221 85887 86096 86322 86472 86682 87273 87313 87386 87634 87825 87889 88192 88446 88510 88710 88728 88957 89318 89441 89562 89636 89696 89849 89857 89890 90159 90391 90439 90612 90805 91261 91311 91405 91427 91690 91691 92284 92377 92481 92507 92808 92955 93305 93308 93341 93383 93467 93519 93962 94003 94040 94134 94212 94394 94524 94541 94606 94629 94645 94837 95106 95471 95517 95762 95849 95961 96008 96686 96835 97071 97151 97413 97414 97719 98379 99064 99228 99816
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 '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.
Cluster timing data:
TIME: Cluster Init. : 0.3248 s ( 0.55%)
TIME: Pairwise Calc.: 0.0787 s ( 0.13%)
TIME: Clustering : 0.0447 s ( 0.08%)
TIME: Cluster Post. : 58.7258 s ( 99.24%)
TIME: Total: 59.1740 s
TIME: Analyses took 59.1740 seconds.
DATASETS (3 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 100000
_DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 100000 (78.000 MB) Box Coords, 63 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 : 1145.2184 s ( 95.08%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 59.1740 s ( 4.91%)
TIME: Data File Write : 0.1349 s ( 0.01%)
TIME: Other : 0.0004 s ( 0.00%)
TIME: Run Total 1204.5278 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 1206.8114 seconds.
--------------------------------------------------------------------------------
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.