CPPTRAJ: Trajectory Analysis. V16.00b OpenMP
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| Date/time: 06/02/16 15:56:38
| Available memory: 15.887 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, 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= 63.1310 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 (185760000)
Estimated pair-wise matrix memory usage: > 499.064 kB
Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames.
1% 11% 21% 30% 40% 50% 61% 70% 80% 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: 495 points changed cluster assignment.
Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 1: 11 points changed cluster assignment.
Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 2: 2 points changed cluster assignment.
Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 3: 2 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: 5 clusters 100000 frames
#Cluster 0 has average-distance-to-centroid 1.152809
#Cluster 1 has average-distance-to-centroid 1.240610
#Cluster 2 has average-distance-to-centroid 1.312312
#Cluster 3 has average-distance-to-centroid 1.809370
#Cluster 4 has average-distance-to-centroid 1.852138
#DBI: 1.672432
#pSF: 19367.517248
#Algorithm: Kmeans nclusters 5 maxit 100
#Representative frames: 9420 61124 69056 19409 88794
#Sieve value: 200 (random)
#Sieved frames: 213 255 384 949 997 1017 1294 1385 1790 2023 2148 2396 2791 3077 3847 3865 3867 3888 3961 4032 4129 4221 4443 4528 4618 4910 5152 5214 5400 5563 5723 5888 6015 6136 6214 6437 6483 6741 7157 7578 8358 8402 8490 8550 8579 8982 9026 9104 9221 9420 9488 9842 10184 10353 10475 10552 10782 11054 11101 12235 12427 12822 12971 13084 13262 13869 14002 14304 14397 14442 14459 15172 15231 15270 15525 15535 15977 16090 16485 16555 16718 16901 17123 17189 17392 17435 17469 17648 17763 17899 17986 18061 18180 18340 18482 18514 18520 18710 18823 19303 19400 19409 19778 19861 20025 20194 20354 20541 20662 20999 21003 21163 21234 21433 21530 21598 21656 21809 21860 22129 22132 22876 23729 23955 24133 24190 24216 24292 24310 24487 24830 25021 25334 25520 25703 25848 26216 26347 26370 26615 26696 26799 27199 27261 27399 27448 27478 27566 27698 27732 28045 28053 28105 28126 28264 28314 28438 28572 28753 28969 29036 29297 30022 30056 30733 30748 31313 31533 31754 31847 31864 32134 32425 32590 32794 33074 33098 33436 33510 33663 33697 33927 34161 34205 34824 35105 35141 35327 35512 35676 35754 35845 36259 36429 36737 37007 37108 37151 37311 37608 37659 37909 38082 38362 38369 38491 38699 39049 39139 39915 39957 40061 40194 40606 40992 41218 41335 41579 41650 41922 41994 42055 42558 42704 42783 42788 42808 43447 43495 43507 43790 43821 44088 44335 44376 44413 44555 45391 45416 45598 45959 46205 46210 46444 46655 46688 46778 46780 46807 46823 46972 47384 47746 48261 48534 48796 48809 49408 49572 49781 50421 50546 51029 51066 51126 51390 51409 51602 51687 51811 51851 51982 52174 52666 52790 53683 54526 54692 54729 55008 55041 55193 55270 55414 55419 55497 55699 56305 56602 56614 56988 56997 57021 57286 57414 57471 57556 57765 58307 58344 58418 58471 58571 58920 58946 59596 59656 59703 60163 60177 60851 61124 61310 61411 61894 62002 62048 62136 62598 62703 62821 62867 63162 63456 63671 63716 63901 63955 64124 64442 64759 64809 64992 65142 65248 65324 65480 65705 65777 65784 66150 66204 66378 66523 66821 67026 67244 67393 67650 68024 68144 68229 68240 68749 68821 68831 68978 69020 69056 69098 69517 69702 69793 70323 70642 71301 71417 71794 72051 72342 72428 72599 73313 73841 74140 74149 74315 74540 74541 74859 75479 75523 75935 76130 76618 76736 76866 76992 77850 78111 78352 78373 78533 78545 78621 78741 78747 78902 78990 79937 80106 80138 80597 80601 80824 81217 81267 81467 81554 81986 82614 82631 83186 83245 83373 83550 84006 84106 84254 84277 84316 84518 85203 85679 86317 86487 86557 86666 86762 87113 87227 87252 87355 87669 87672 87916 87986 88088 88687 88794 88806 88811 88856 88974 89332 89508 89520 90413 91055 91216 91441 91915 91943 92016 92059 92174 92525 92826 92912 93218 93578 93786 93949 93973 94265 94375 94462 94581 94658 94731 94741 94804 94817 95201 95310 95398 95421 95435 95790 95891 96011 96225 96558 96806 97038 97159 97603 98062 98227 98290 98298 98533 98563 98603 98642 98676 98775 98914 99574 99743
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. : 0.4260 s ( 0.47%)
TIME: Pairwise Calc.: 0.4525 s ( 0.50%)
TIME: Clustering : 0.0580 s ( 0.06%)
TIME: Cluster Post. : 90.3158 s ( 98.97%)
TIME: Total: 91.2524 s
TIME: Analyses took 91.2524 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 : 1584.0079 s ( 94.54%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 91.2524 s ( 5.45%)
TIME: Data File Write : 0.1737 s ( 0.01%)
TIME: Other : 0.0001 s ( 0.00%)
TIME: Run Total 1675.4341 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 1680.2984 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.