In [1]:

    

#!/usr/bin/env python3

# core openmm imports
from simtk.openmm import *
from simtk.openmm.app import *
from simtk.unit import *

from sys import stdout

# mdtraj provides extended trajectory output formats such as HDF5 and NetCDF
import mdtraj as mdt

# ngl view permits visualization of the system
import nglview as ng


    

In [2]:

    

# Input Files
print('Parsing PDB file...')
pdb = PDBFile('input/ala2.pdb')

print('Parsing FF file(s)...')
forcefield = ForceField('amber99sbildn.xml')


    

    




Parsing PDB file...
Parsing FF file(s)...

In [3]:

    

# System Configuration
nonbondedMethod = CutoffNonPeriodic
nonbondedCutoff = 1.4*nanometers
constraints = HBonds
constraintTolerance = 0.00001


    

In [4]:

    

# Integration Options
dt = 0.002*picoseconds
temperature = 300.00*kelvin
friction = 2/picosecond

integrator = LangevinIntegrator(temperature, friction, dt)
integrator.setConstraintTolerance(constraintTolerance)


    

In [5]:

    

platform = Platform.getPlatformByName('CPU')
platformProperties = {'CpuThreads':'1'}

#platform = Platform.getPlatformByName('OpenCL')
#platformProperties = {'OpenCLPrecision':'mixed'}

#platform = Platform.getPlatformByName('CUDA')
#platformProperties = {'CudaPrecision': 'mixed'}


    

In [6]:

    

# Prepare the Simulation
print('Building system...')
topology = pdb.topology
positions = pdb.positions
system = forcefield.createSystem(topology, nonbondedMethod=nonbondedMethod,
                                 nonbondedCutoff=nonbondedCutoff,
                                 constraints=constraints)

simulation = Simulation(topology, system, integrator,
                        platform, platformProperties)

# set initial positions to what was one obtained from PDB parsing
simulation.context.setPositions(positions)


    

    




Building system...

In [7]:

    

# Minimize energy
print('Performing energy minimization...')
simulation.minimizeEnergy()

# after minimization of the energy, set initial velocities to random distribution for a given temperature
simulation.context.setVelocitiesToTemperature(temperature)


    

    




Performing energy minimization...

In [8]:

    

equilibrationSteps = 25000
printFreq = 250

# reporters objects are used for terminal IO and trajectory IO
#  here we use the StateDataReporter for regularly printing simulation time, energy, etc. to a terminal
simulation.reporters.append(StateDataReporter(stdout, printFreq, step=True, 
    time=True, potentialEnergy=True, kineticEnergy=True, temperature=True))

print('Equilibrating...')
simulation.step(equilibrationSteps)


    

    




Equilibrating...
#"Step","Time (ps)","Potential Energy (kJ/mole)","Kinetic Energy (kJ/mole)","Temperature (K)"
250,0.5000000000000003,61.69791289546146,63.21198316112848,298.14294400719956
500,1.0000000000000007,111.23739585845304,48.729957426705525,229.8376390361001
750,1.500000000000001,85.08710300300032,77.65620845498577,366.269961032384
1000,2.0000000000000013,81.31684654038045,57.52660940514127,271.32755261106865
1250,2.4999999999999463,88.79200073782332,64.26787246355815,303.12310646104385
1500,2.999999999999891,65.51939790115708,68.56565182010557,323.3938292888379
1750,3.499999999999836,88.2968232537487,51.685363422931104,243.77698092014128
2000,3.999999999999781,79.67389740505163,61.7413243969083,291.2064975983448
2250,4.499999999999726,68.46983221550656,69.53919459548648,327.9855996249961
2500,4.999999999999671,73.53631167257123,65.57428315257629,309.2848674030081
2750,5.499999999999616,90.14644581770472,55.778951198850514,263.0846224468038
3000,5.999999999999561,69.82654629685305,42.18960038638353,198.98966994313037
3250,6.499999999999506,75.99792496467366,52.10053271625355,245.7351507035038
3500,6.999999999999451,88.20599996702498,51.82668488210659,244.44353168762112
3750,7.499999999999396,82.5696228962187,43.212068451516,203.81219921443784
4000,7.999999999999341,62.614450926851816,61.87118748859114,291.8190043183683
4250,8.499999999999508,89.52967248971183,50.623192971494454,238.76719306675975
4500,8.999999999999675,82.91286854561069,37.22249020987073,175.56200991451232
4750,9.499999999999842,93.21407261494207,53.74057897602852,253.47052295010647
5000,10.000000000000009,63.38685082655887,71.97412700987445,339.4700980093247
5250,10.500000000000176,75.08458175189867,48.30287298858524,227.82327078892345
5500,11.000000000000343,89.7629065467668,59.48986728128959,280.58737098360984
5750,11.50000000000051,84.90793858871487,72.36700463611261,341.3231278663793
6000,12.000000000000677,84.48926544153983,51.32523934891804,242.0784350706868
6250,12.500000000000844,69.96267884916419,58.299446974037224,274.9726853296969
6500,13.00000000000101,72.03980399867814,59.47381465532708,280.5116578525836
6750,13.500000000001178,87.50890467308534,63.2337665645551,298.2456866788154
7000,14.000000000001345,82.3334894194986,60.700774969363685,286.2986865441913
7250,14.500000000001512,61.431662398915236,46.99774251062157,221.6675480358222
7500,15.000000000001679,85.71027158211668,56.62913704901153,267.0945727702125
7750,15.500000000001846,98.47342229180482,88.45762275388097,417.21545107191184
8000,16.00000000000201,81.72673275714662,82.20849565154509,387.7410846845065
8250,16.500000000001734,88.86474112226072,68.95593409053107,325.23461800134936
8500,17.000000000001457,77.38451540160248,74.7210054052834,352.42590750432896
8750,17.50000000000118,89.30605565549735,48.42817167445427,228.41424922714143
9000,18.000000000000902,84.03743633861802,59.1727023273432,279.09144428780525
9250,18.500000000000625,76.50139701746366,67.77777364554004,319.6777566909379
9500,19.000000000000348,68.78490464961214,71.19539756432225,335.7971759165276
9750,19.50000000000007,87.26798606873314,53.27798315150065,251.28866321223654
10000,19.999999999999794,98.20278476506594,47.2408553211238,222.8142035499237
10250,20.499999999999517,85.31210673361923,58.97960148279463,278.18067307948485
10500,20.99999999999924,92.66538845365909,64.47200597809467,304.0859138901245
10750,21.499999999998963,76.73768118869658,63.212412098578966,298.14496711528585
11000,21.999999999998685,84.91905696879348,65.3815288008079,308.37573044775803
11250,22.49999999999841,96.65359556956764,66.09652911359927,311.7480704308006
11500,22.99999999999813,95.50357525709721,57.3109377702182,270.31032497543345
11750,23.499999999997854,87.36811808347245,66.15015714014716,312.0010100937681
12000,23.999999999997577,91.48481688223842,81.49144665243357,384.3590819549356
12250,24.4999999999973,71.78833509961166,69.35528922458961,327.1181993955465
12500,24.999999999997023,109.19558095578594,71.70784540595865,338.214165552277
12750,25.499999999996746,82.34226493618945,101.26002551096397,477.5987179381507
13000,25.99999999999647,93.46297309385437,68.35630017965288,322.4064102695958
13250,26.49999999999619,79.35991004170896,86.47726172398245,407.8749646937824
13500,26.999999999995914,100.52425297556834,65.69401129521344,309.8495720545829
13750,27.499999999995637,79.69745098334843,67.93096956705268,320.40031404107276
14000,27.99999999999536,87.42575516936216,70.0613209062615,330.44823831553174
14250,28.499999999995083,95.67812214784882,60.50629581719359,285.38141446892325
14500,28.999999999994806,94.77123676900052,71.3518788431582,336.5352288429046
14750,29.49999999999453,73.35552954948264,67.08879674291386,316.42815761447275
15000,29.99999999999425,79.99011254806584,84.7959010463449,399.9447306258049
15250,30.499999999993975,93.61341697953215,73.30527006293556,345.74851056478497
15500,30.999999999993697,90.87216765121252,54.80094870827433,258.47181760814686
15750,31.49999999999342,77.5296810600511,69.8177433211559,329.299390665357
16000,31.999999999993143,85.86200793581354,85.94270136086725,405.35368008224793
16250,32.499999999993754,95.3861981144198,80.76983107188582,380.95554068211146
16500,32.999999999994365,69.6332950519104,77.81883907889858,367.03701769750234
16750,33.49999999999498,104.03188106350638,63.99377639695942,301.8303166425654
17000,33.99999999999559,79.24872552648141,64.78324663172296,305.55389828369954
17250,34.4999999999962,76.61363839907501,69.19053021315112,326.3411040685928
17500,34.99999999999681,56.33409607864624,75.71743237060298,357.12561243482105
17750,35.49999999999742,75.45540377248082,63.24264852279105,298.28757894424655
18000,35.99999999999803,103.79341530735277,57.284879594430464,270.1874200948033
18250,36.49999999999864,98.52079347191533,64.48693285787832,304.15631737473274
18500,36.999999999999254,97.6233281285584,50.684140630576266,239.05465619637997
18750,37.499999999999865,88.61654936116948,51.99161144944207,245.22141730157284
19000,38.000000000000476,72.18357353561399,54.818591039746835,258.55502867638614
19250,38.50000000000109,69.24738218811858,66.67206060995069,314.462597742081
19500,39.0000000000017,73.1101677522825,70.40892381733406,332.08772738184496
19750,39.50000000000231,84.05473836690282,83.72929661009212,394.9140296287336
20000,40.00000000000292,69.89370469200699,54.25363668107372,255.89038904160122
20250,40.50000000000353,84.55110172267527,59.412887245834355,280.22429023131167
20500,41.00000000000414,86.40432289871902,57.209478132767586,269.83178477633345
20750,41.50000000000475,68.57764905459047,68.95537700434161,325.231990472386
21000,42.000000000005365,77.34484199397491,42.72520999490777,201.51590338081436
21250,42.500000000005976,86.11940516018507,55.379459186637376,261.2003954589401
21500,43.00000000000659,73.05069293366392,40.78802454285778,192.3790570918774
21750,43.5000000000072,94.40342120647765,72.76739866066771,343.2116092471875
22000,44.00000000000781,84.27701247968892,65.33904911474536,308.1753725720859
22250,44.50000000000842,76.01841052383836,75.63565526745106,356.7399060376029
22500,45.00000000000903,80.38271967726784,52.74120835437849,248.75693409570283
22750,45.50000000000964,88.80079304377705,53.722877721110926,253.38703396605888
23000,46.00000000001025,73.90168591246109,51.75856499954856,244.1222403546233
23250,46.500000000010864,67.42609347451435,44.531313594342095,210.03449459388804
23500,47.000000000011475,60.679891561333406,77.18442914492267,364.04478685828224
23750,47.500000000012086,71.50048502970203,81.05996302399738,382.32396467432517
24000,48.0000000000127,106.88739532301898,43.16736428423655,203.6013494455244
24250,48.50000000001331,93.2355802803819,62.05849295734448,292.70244130436544
24500,49.00000000001392,53.68616207224801,55.24369213517034,260.56004237398184
24750,49.50000000001453,76.9775567849949,57.80914216687797,272.6601345860393
25000,50.00000000001514,58.03946168087481,52.417665407303,247.2309252295046

In [9]:

    

# reste step and time counters
simulation.currentStep = 0
simulation.context.setTime(0.0)

# save the equilibration results to file : state is platform independent but less precise, checkpoint file
#  contains the binary representation but it is platform dependent
simulation.saveState('output/eq.state')
simulation.saveCheckpoint('output/eq.chk')

simsteps = 5e5 # 1 ns
svfreq=500

simulation.reporters = []

simulation.reporters.append(StateDataReporter(stdout, svfreq, step=True, 
    time=True, potentialEnergy=True, kineticEnergy=True, totalEnergy=True,
    temperature=True, progress=True,remainingTime=True, speed=True, totalSteps=simsteps))

hdf5rep = mdt.reporters.HDF5Reporter('output/sim_1ns.hdf5', svfreq,
                                     coordinates=True, time=True, cell=True, potentialEnergy=True,
                                     kineticEnergy=True, temperature=True, velocities=True)

# dcdrep = DCDReporter('output/sim_1ns.dcd', svfreq)

simulation.reporters.append(hdf5rep)
# simulation.reporters.append(dcdrep)

simulation.step(simsteps)

simulation.saveState('output/sim_1ns.state')
simulation.saveCheckpoint('output/sim_1ns.chk')

hdf5rep.close()


    

    




#"Progress (%)","Step","Time (ps)","Potential Energy (kJ/mole)","Kinetic Energy (kJ/mole)","Total Energy (kJ/mole)","Temperature (K)","Speed (ns/day)","Time Remaining"
0.1%,500,1.0000000000000007,67.27385802639705,61.954839624287715,129.22869765068475,292.21355441412294,0,--
0.2%,1000,2.0000000000000013,98.13560299778823,59.803892084306476,157.9394950820947,282.06848697745687,1.99e+03,0:43
0.3%,1500,2.999999999999891,100.61851531835615,65.9593000822561,166.57781540061225,311.10082183390693,2.18e+03,0:39
0.4%,2000,3.999999999999781,108.23932273014964,85.00164740479624,193.24097013494588,400.915145125712,2.26e+03,0:38
0.5%,2500,4.999999999999671,93.44725826809585,54.69430864399618,148.14156691209203,257.9688436287992,2.28e+03,0:37






    




/home/fhedin/bin/anaconda3/envs/openmm-tutorials/lib/python3.5/site-packages/mdtraj/formats/hdf5.py:198: UserWarning: The .h5 extension is recommended.
  warnings.warn('The .h5 extension is recommended.')






    




0.6%,3000,5.999999999999561,70.67214961713992,37.78762599996238,108.45977561710231,178.2275052809885,2.21e+03,0:38
0.7%,3500,6.999999999999451,84.03150992810856,93.54793655317752,177.57944648128608,441.22420805354704,2.17e+03,0:39
0.8%,4000,7.999999999999341,76.6771912568689,85.53517589769588,162.2123671545648,403.43156286219335,2.21e+03,0:38
0.9%,4500,8.999999999999675,94.12297619783577,77.99957999992697,172.12255619776272,367.889492617655,2.19e+03,0:39
1.0%,5000,10.000000000000009,100.64484171631855,60.300625463851134,160.9454671801697,284.4113584514713,2.21e+03,0:38
1.1%,5500,11.000000000000343,72.76607580604427,61.95498190811311,134.72105771415738,292.21422550394595,2.16e+03,0:39
1.2%,6000,12.000000000000677,87.38803436042221,67.71524088867804,155.10327524910025,319.3828173567265,2.13e+03,0:40
1.3%,6500,13.00000000000101,86.83957228135729,76.20280355420523,163.04237583556252,359.41489346001157,2.1e+03,0:40
1.4%,7000,14.000000000001345,62.8355023327164,59.49573872327135,122.33124105598776,280.6150639764645,2.08e+03,0:41
1.5%,7500,15.000000000001679,96.89788152295746,65.25425956442793,162.1521410873854,307.77545779503725,2.06e+03,0:41
1.6%,8000,16.00000000000201,68.96517607950628,61.16306129654992,130.1282373760562,288.4790865200986,2.04e+03,0:41
1.7%,8500,17.000000000001457,84.66238910536084,99.25499426827521,183.91738337363606,468.1418730864732,2.05e+03,0:41
1.8%,9000,18.000000000000902,78.98263295996728,75.08255473676697,154.06518769673426,354.13117566238657,2.07e+03,0:41
1.9%,9500,19.000000000000348,72.0266805738809,58.60075873320798,130.62743930708888,276.39383952310624,2.08e+03,0:40
2.0%,10000,19.999999999999794,99.56610331786773,79.81552417886618,179.38162749673393,376.45449748835506,2.1e+03,0:40
2.1%,10500,20.99999999999924,77.43732248371992,107.8960500835724,185.33337256729232,508.8979084340161,2.1e+03,0:40
2.2%,11000,21.999999999998685,101.215548791575,83.61686673196441,184.8324155235394,394.3837476602985,2.11e+03,0:40
2.3%,11500,22.99999999999813,71.62851289283975,48.86753727455247,120.49605016739221,230.48654227915438,2.12e+03,0:39
2.4%,12000,23.999999999997577,87.85268458712613,53.93846122608761,141.79114581321375,254.40384593174747,2.13e+03,0:39
2.5%,12500,24.999999999997023,68.78023827532826,51.80610567214816,120.58634394747642,244.34646866356272,2.14e+03,0:39
2.6%,13000,25.99999999999647,69.79636627821822,54.94144084902273,124.73780712724096,259.134456847701,2.15e+03,0:39
2.7%,13500,26.999999999995914,74.81222348796666,60.48779229187036,135.30001577983703,285.29414153049447,2.16e+03,0:38
2.8%,14000,27.99999999999536,91.44272880882559,72.75616514018553,164.1988939490111,343.1586257035517,2.17e+03,0:38
2.9%,14500,28.999999999994806,73.65905890111628,77.87149195056082,151.5305508516771,367.28535798652314,2.16e+03,0:38
3.0%,15000,29.99999999999425,78.06256216600238,81.5383137804908,159.60087594649318,384.58013345241085,2.17e+03,0:38
3.1%,15500,30.999999999993697,94.90938471363657,57.95987089470153,152.8692556083381,273.37105527563745,2.17e+03,0:38
3.2%,16000,31.999999999993143,75.54997368605198,54.66139982300454,130.21137350905653,257.8136272871565,2.18e+03,0:38
3.3%,16500,32.999999999994365,85.72994572767311,49.05503163463295,134.78497736230605,231.37087018192955,2.18e+03,0:38
3.4%,17000,33.99999999999559,71.43960814697206,57.86350106108343,129.3031092080555,272.91652142823153,2.19e+03,0:38
3.5%,17500,34.99999999999681,64.68801532109083,45.203047915916656,109.89106323700749,213.202768047901,2.19e+03,0:38
3.6%,18000,35.99999999999803,91.82243617888614,83.50517977915838,175.32761595804453,393.8569697417526,2.2e+03,0:37
3.7%,18500,36.999999999999254,81.70286542190885,66.27403641111628,147.97690183302512,312.58529378020233,2.2e+03,0:37
3.8%,19000,38.000000000000476,86.12302093760013,55.49126485683148,141.61428579443162,261.72773331485575,2.21e+03,0:37
3.9%,19500,39.0000000000017,77.90047614603449,71.17823463128691,149.07871077732142,335.7162259585124,2.21e+03,0:37
4.0%,20000,40.00000000000292,91.33399011269236,67.99959437191411,159.3335844846065,320.7239868690736,2.21e+03,0:37
4.1%,20500,41.00000000000414,91.04495671990446,92.22589711023177,183.27085383013622,434.9887331973197,2.22e+03,0:37
4.2%,21000,42.000000000005365,98.52054416381515,62.665522999864805,161.18606716367995,295.56553331520297,2.22e+03,0:37
4.3%,21500,43.00000000000659,74.63028067791717,55.51117184807193,130.1414525259891,261.8216257807768,2.22e+03,0:37
4.4%,22000,44.00000000000781,90.31458644401536,71.12661662274014,161.44120306675552,335.47276666072867,2.22e+03,0:37
4.5%,22500,45.00000000000903,113.68954311988506,58.68997050180778,172.37951362169284,276.8146119463133,2.22e+03,0:37
4.6%,23000,46.00000000001025,84.79520698812317,77.53748526466403,162.33269225278718,365.7099962960424,2.23e+03,0:37
4.7%,23500,47.000000000011475,114.1678776359418,47.314948191859884,161.4828258278017,223.163666824235,2.21e+03,0:37
4.8%,24000,48.0000000000127,76.36252670640533,58.79241244348407,135.1549391498894,277.2977852396322,2.2e+03,0:37
4.9%,24500,49.00000000001392,79.08917999908803,78.99329202942252,158.08247202851055,372.57639239762204,2.21e+03,0:37
5.0%,25000,50.00000000001514,87.48137664474639,67.85159177292412,155.33296841767051,320.025924122472,2.2e+03,0:37
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9.0%,45000,89.99999999997165,91.15021451562905,48.0177813523512,139.16799586798024,226.47861973562578,2.16e+03,0:36
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10.0%,50000,99.99999999994834,68.75127518533175,53.75138131958573,122.50265650491748,253.5214728230461,2.14e+03,0:36
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10.9%,54500,108.99999999992737,94.71787213805827,52.52519027863013,147.2430624166884,247.73807245204546,2.12e+03,0:36
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18.0%,90000,180.00000000013137,84.37788686562016,62.165534796279246,146.5434216618994,293.2073102769241,2.16e+03,0:32
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18.6%,93000,186.00000000016001,82.93641901904178,56.89375208536484,139.83017110440662,268.3426447657682,2.16e+03,0:32
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20.6%,103000,206.0000000002555,99.62087833722155,45.94571333963537,145.56659167685692,216.705592113323,2.15e+03,0:31
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21.3%,106500,213.00000000028894,73.08566648247199,51.79135283713854,124.87701931961053,244.27688607111327,2.15e+03,0:31
21.4%,107000,214.0000000002937,60.07765318825656,75.89070297693819,135.96835616519473,357.9428531872748,2.15e+03,0:31
21.5%,107500,215.00000000029848,97.03682802322658,81.86040955111632,178.8972375743429,386.09931662788216,2.16e+03,0:31
21.6%,108000,216.00000000030326,92.09141943956627,80.59273813647972,172.684157576046,380.12027169537095,2.15e+03,0:31
21.7%,108500,217.00000000030803,92.79539930082194,65.8940444725579,158.68944377337982,310.79304000812846,2.15e+03,0:31
21.8%,109000,218.0000000003128,97.7939082786499,51.37264906591626,149.16655734456614,242.30204572002154,2.15e+03,0:31
21.9%,109500,219.00000000031758,108.4580204477883,59.5865770502117,168.044597498,281.0435081553736,2.15e+03,0:31
22.0%,110000,220.00000000032236,102.32724180149572,75.78096943121675,178.10821123271245,357.425288625278,2.15e+03,0:31
22.1%,110500,221.00000000032713,83.21835215435101,60.36887743502671,143.58722958937773,284.7332727880095,2.15e+03,0:31
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22.3%,111500,223.00000000033668,67.88665329769972,50.309843487384214,118.19649678508394,237.28926225326782,2.16e+03,0:31
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22.5%,112500,225.00000000034623,95.72457465254266,65.64024556439568,161.36482021693834,309.5959829015287,2.16e+03,0:31
22.6%,113000,226.000000000351,84.8619854698684,68.27742866134233,153.13941413121074,322.03440822992746,2.16e+03,0:31
22.7%,113500,227.00000000035578,82.71739532048849,56.211296722854605,138.9286920433431,265.12380490729305,2.16e+03,0:30
22.8%,114000,228.00000000036056,87.3689317946801,59.049672803049354,146.41860459772946,278.51116848030097,2.16e+03,0:30
22.9%,114500,229.00000000036533,92.61114752100173,69.27643544823445,161.88758296923618,326.74628103682824,2.16e+03,0:30
23.0%,115000,230.0000000003701,86.6144170800497,75.78880170967578,162.40321878972549,357.4622300158385,2.16e+03,0:30
23.1%,115500,231.00000000037488,89.58841466734783,49.94102712469335,139.52944179204118,235.5497187257314,2.16e+03,0:30
23.2%,116000,232.00000000037966,81.86189842386048,54.548567335570056,136.41046575943054,257.281446388835,2.16e+03,0:30
23.3%,116500,233.00000000038443,109.194856561153,47.408295894725235,156.60315245587825,223.60394661861582,2.16e+03,0:30
23.4%,117000,234.0000000003892,76.0508918687263,76.6525205984704,152.7034124671967,361.5360096921295,2.16e+03,0:30
23.5%,117500,235.00000000039398,80.67120442633902,55.41832522870759,136.0895296550466,261.38370937546733,2.16e+03,0:30
23.6%,118000,236.00000000039876,105.37076770395632,83.93276186848243,189.30352957243875,395.8736851893738,2.16e+03,0:30
23.7%,118500,237.00000000040353,75.59835078868207,70.15256165080642,145.7509124394885,330.8785805201528,2.16e+03,0:30
23.8%,119000,238.0000000004083,92.91115819879082,63.61331197335703,156.52447017214786,300.03583436768287,2.16e+03,0:30
23.9%,119500,239.00000000041308,89.75399180897514,47.89181584631882,137.64580765529396,225.88449620186287,2.16e+03,0:30
24.0%,120000,240.00000000041786,82.164326202632,40.96028981562577,123.12461601825777,193.19155613090194,2.16e+03,0:30
24.1%,120500,241.00000000042263,81.66775383693849,54.73878674983039,136.40654058676887,258.17862716594084,2.16e+03,0:30
24.2%,121000,242.0000000004274,78.40309575263298,60.17983379397732,138.5829295466103,283.84163761268786,2.16e+03,0:30
24.3%,121500,243.00000000043218,99.06047786235865,59.525876484846535,158.5863543472052,280.7572104574396,2.16e+03,0:30
24.4%,122000,244.00000000043696,96.87535371735797,63.52239313104382,160.3977468484018,299.6070104333998,2.16e+03,0:30
24.5%,122500,245.00000000044173,60.98454440632315,79.90401356591273,140.8885579722359,376.87186275753515,2.16e+03,0:30
24.6%,123000,246.0000000004465,125.01823392782603,53.3725001203428,178.39073404816884,251.73445791665839,2.16e+03,0:30
24.7%,123500,247.00000000045128,86.89367746080812,69.3141024200308,156.20777988083893,326.92393946963796,2.16e+03,0:30
24.8%,124000,248.00000000045605,103.67919364113308,73.97114074834731,177.6503343894804,348.8891278425361,2.16e+03,0:30
24.9%,124500,249.00000000046083,69.22431308666029,68.73472503125218,137.95903811791248,324.1912727861493,2.16e+03,0:30
25.0%,125000,250.0000000004656,82.31272644683952,65.23280010290144,147.54552654974094,307.67424301397256,2.16e+03,0:29
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25.3%,126500,253.00000000047993,79.1814784947791,70.1420775616293,149.3235560564084,330.8291317122499,2.16e+03,0:29
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25.6%,128000,256.00000000049425,113.98461655975174,79.25996991756824,193.24458647731998,373.83419395196853,2.16e+03,0:29
25.7%,128500,257.000000000499,78.97486628059508,73.48151349972888,152.45637978032397,346.5797728425965,2.17e+03,0:29
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25.9%,129500,259.0000000005086,84.80352977008599,60.51537118660075,145.31890095668675,285.4242189692362,2.17e+03,0:29
26.0%,130000,260.00000000051335,86.78489500435333,61.587134888987805,148.37202989334114,290.4792539409317,2.17e+03,0:29
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26.3%,131500,263.0000000005277,83.60919422153779,75.78410222501913,159.39329644655692,357.4400646269235,2.17e+03,0:29
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26.6%,133000,266.000000000542,95.49740812051016,65.07860489117868,160.57601301168884,306.9469724542489,2.17e+03,0:29
26.7%,133500,267.0000000005468,97.03922044214698,73.91896114435937,170.95818158650636,348.64301974764464,2.17e+03,0:29
26.8%,134000,268.00000000055155,81.31102969036922,57.41174727534997,138.7227769657192,270.7857987881642,2.17e+03,0:29
26.9%,134500,269.0000000005563,64.46594662969409,81.45599523411688,145.92194186381096,384.1918733071825,2.17e+03,0:29
27.0%,135000,270.0000000005611,89.15858350156873,72.83158246308155,161.99016596465026,343.5143358324373,2.17e+03,0:29
27.1%,135500,271.0000000005659,99.30134957113938,50.086175900864895,149.38752547200428,236.23432125333315,2.17e+03,0:28
27.2%,136000,272.00000000057065,77.04655195134418,56.35342027808631,133.3999722294305,265.79413880682506,2.17e+03,0:28
27.3%,136500,273.0000000005754,77.78332217192676,53.00990847042618,130.79323064235294,250.0242736039307,2.17e+03,0:28
27.4%,137000,274.0000000005802,72.43435516994799,69.03596011023322,141.4703152801812,325.61206531304595,2.17e+03,0:28
27.5%,137500,275.000000000585,89.60138503735638,40.91509026746798,130.51647530482435,192.97836986966396,2.17e+03,0:28
27.6%,138000,276.00000000058975,63.903894756691855,67.1854422288237,131.08933698551556,316.8839915917223,2.17e+03,0:28
27.7%,138500,277.0000000005945,73.21961640534361,79.34351634752042,152.56313275286402,374.22824548051716,2.17e+03,0:28
27.8%,139000,278.0000000005993,84.25317656524678,63.009580182911996,147.26275674815878,297.18829875192466,2.17e+03,0:28
27.9%,139500,279.0000000006041,108.41700433993236,58.57304741259002,166.9900517525224,276.26313749007073,2.17e+03,0:28
28.0%,140000,280.00000000060885,87.15918314225105,74.16812496905692,161.32730811130796,349.8182152172451,2.18e+03,0:28
28.1%,140500,281.0000000006136,112.67298960025397,68.2892069090892,180.9621965093432,322.0899610109492,2.18e+03,0:28
28.2%,141000,282.0000000006184,89.53500418521631,74.85289570665779,164.3878998918741,353.04797567513015,2.18e+03,0:28
28.3%,141500,283.0000000006232,90.88785964020003,91.7562572368693,182.64411687706934,432.7736497991206,2.18e+03,0:28
28.4%,142000,284.00000000062795,69.4547274281407,39.7751034626745,109.22983089081521,187.60155672263565,2.18e+03,0:28
28.5%,142500,285.0000000006327,86.66992266799792,82.54419180103903,169.21411446903696,389.3244148269399,2.18e+03,0:28
28.6%,143000,286.0000000006375,95.98537931504602,60.52661013290156,156.51198944794757,285.47722810405673,2.18e+03,0:28
28.7%,143500,287.0000000006423,84.91859748078319,69.09522039006197,154.01381787084517,325.891569821642,2.18e+03,0:28
28.8%,144000,288.00000000064705,90.45653342644434,79.4812724174092,169.93780584385354,374.8779798849387,2.18e+03,0:28
28.9%,144500,289.0000000006518,88.85924184897699,69.05185538244375,157.91109723142074,325.68703627607624,2.18e+03,0:28
29.0%,145000,290.0000000006566,79.6041604515778,95.06117567764859,174.66533612922638,448.3614871736572,2.18e+03,0:28
29.1%,145500,291.0000000006614,114.52818673626658,78.99650555491729,193.52469229118387,372.5915491749251,2.18e+03,0:28
29.2%,146000,292.00000000066615,97.6276821585606,50.73470929344172,148.36239145200233,239.2931661950741,2.18e+03,0:28
29.3%,146500,293.0000000006709,88.91941641394078,68.11095674173676,157.03037315567752,321.24923387336247,2.18e+03,0:28
29.4%,147000,294.0000000006757,69.20688208961474,51.99847365457694,121.20535574419168,245.25378328566288,2.18e+03,0:27
29.5%,147500,295.0000000006805,112.93716301939679,54.90814120919779,167.84530422859459,258.97739718661614,2.18e+03,0:27
29.6%,148000,296.00000000068525,76.46179999886738,75.45038534907073,151.9121853479381,355.866069841686,2.18e+03,0:27
29.7%,148500,297.00000000069,93.67926344481216,52.265407105180714,145.94467054999288,246.5127902150001,2.18e+03,0:27
29.8%,149000,298.0000000006948,68.69180375373298,51.000885688850964,119.69268944258394,240.54860243016657,2.18e+03,0:27
29.9%,149500,299.0000000006996,104.31668487586307,58.4317868246295,162.7484717004926,275.59687382516745,2.18e+03,0:27
30.0%,150000,300.00000000070435,65.02739464691388,72.25638346668968,137.28377811360355,340.80137677628613,2.18e+03,0:27
30.1%,150500,301.0000000007091,77.34699813200409,65.97248786217784,143.31948599418195,311.163022754273,2.18e+03,0:27
30.2%,151000,302.0000000007139,89.38388404743608,73.51085355305287,162.89473760048895,346.71815688685354,2.18e+03,0:27
30.3%,151500,303.00000000071867,94.043197921357,58.33121556542449,152.3744134867815,275.1225237130145,2.18e+03,0:27
30.4%,152000,304.00000000072345,90.81749431095972,106.15786567186754,196.97535998282726,500.6996619652707,2.18e+03,0:27
30.5%,152500,305.0000000007282,72.68848523728313,83.97914711465408,156.66763235193721,396.09246386329806,2.18e+03,0:27
30.6%,153000,306.000000000733,106.3574746112653,44.03403744380398,150.39151205506928,207.68906310935313,2.18e+03,0:27
30.7%,153500,307.00000000073777,92.55469217424877,51.858167517725406,144.41285969197418,244.59202134415622,2.19e+03,0:27
30.8%,154000,308.00000000074255,95.83264900315841,64.73664435051825,160.56929335367664,305.3340959515941,2.19e+03,0:27
30.9%,154500,309.0000000007473,112.29372591693325,55.37331763619505,167.6670435531283,261.1714284840395,2.19e+03,0:27
31.0%,155000,310.0000000007521,78.99749882096737,55.85718636123621,134.85468518220358,263.4536230772554,2.19e+03,0:27
31.1%,155500,311.00000000075687,72.12617570219021,72.43233638497003,144.55851208716024,341.631268806869,2.19e+03,0:27
31.2%,156000,312.00000000076164,82.28567154080949,70.47833729186276,152.76400883267223,332.41512001556447,2.19e+03,0:27
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38.0%,190000,380.00000000108633,84.622290161693,50.774008546590565,135.39629870828355,239.47852337649988,2.21e+03,0:24
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38.5%,192500,385.0000000011102,104.60272584568409,74.86090747956001,179.4636333252441,353.0857636615266,2.21e+03,0:24
38.6%,193000,386.000000001115,71.08409108030273,67.17333170752781,138.25742278783054,316.82687162344956,2.21e+03,0:24
38.7%,193500,387.00000000111976,73.99898231557887,49.35632581406217,123.35530812964103,232.7919414594797,2.21e+03,0:23
38.8%,194000,388.00000000112453,84.27518366098724,56.14616609121183,140.42134975219906,264.816612547681,2.21e+03,0:23
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39.0%,195000,390.0000000011341,69.83054988346011,48.61033663932635,118.44088652278646,229.27344073175675,2.21e+03,0:23
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39.6%,198000,396.00000000116273,111.2673541234709,74.82076094442536,186.08811506789624,352.8964102260202,2.21e+03,0:23
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39.8%,199000,398.0000000011723,72.7051751047182,58.55643209355088,131.26160719826908,276.1847703848761,2.21e+03,0:23
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40.0%,200000,400.00000000118183,116.57908552879627,70.24595719652152,186.8250427253178,331.3190859680784,2.21e+03,0:23
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41.0%,205000,410.0000000012296,82.77887518641427,75.7624202976773,158.54129548409156,357.33780057308167,2.21e+03,0:23
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41.2%,206000,412.00000000123913,78.15740461610862,68.56792308444955,146.72532770055818,323.40454183738115,2.21e+03,0:22
41.3%,206500,413.0000000012439,95.86895021011446,62.02534478235735,157.89429499247183,292.54609603587517,2.21e+03,0:22
41.4%,207000,414.0000000012487,95.83995800804576,58.45746107034626,154.297419078392,275.71796787759814,2.21e+03,0:22
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41.8%,209000,418.0000000012678,91.31276489902716,58.31742655294632,149.63019145197347,275.0574870448133,2.21e+03,0:22
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42.0%,210000,420.00000000127733,84.09676055547104,62.02324617817946,146.12000673365048,292.5361978489079,2.21e+03,0:22
42.1%,210500,421.0000000012821,73.85488876278202,67.44180033330585,141.29668909608787,318.0931192945439,2.21e+03,0:22
42.2%,211000,422.0000000012869,89.73549498423189,55.63336844781034,145.36886343204225,262.3979730518442,2.21e+03,0:22
42.3%,211500,423.00000000129165,78.15507645464783,60.88246726904272,139.03754372369053,287.1556486963146,2.21e+03,0:22
42.4%,212000,424.0000000012964,83.94596275944428,62.64795935654016,146.59392211598444,295.4826933841261,2.21e+03,0:22
42.5%,212500,425.0000000013012,69.71198845055896,42.885821213921915,112.59780966448088,202.27343540690825,2.21e+03,0:22
42.6%,213000,426.000000001306,70.7295764753268,70.10790207571667,140.83747855104346,330.6679410728596,2.21e+03,0:22
42.7%,213500,427.00000000131075,77.2152779965985,69.87254494575227,147.08782294235078,329.5578656708301,2.21e+03,0:22
42.8%,214000,428.0000000013155,88.47020544131526,60.20494011917478,148.67514556049002,283.960053035417,2.21e+03,0:22
42.9%,214500,429.0000000013203,76.35620195370544,72.12930535550248,148.48550730920792,340.2020055764987,2.21e+03,0:22
43.0%,215000,430.0000000013251,85.0444294603455,58.32977933403954,143.37420879438503,275.1157496453145,2.21e+03,0:22
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43.3%,216500,433.0000000013394,81.54965733132494,62.907642005197886,144.45729933652282,296.70750149022604,2.21e+03,0:22
43.4%,217000,434.0000000013442,97.26163118360972,59.16447232618741,156.42610350979714,279.0526270153347,2.21e+03,0:22
43.5%,217500,435.00000000134895,75.2922850146665,65.02034956487569,140.3126345795422,306.67220786659465,2.21e+03,0:22
43.6%,218000,436.0000000013537,84.2571044102668,78.48327557826617,162.740379988533,370.1708705545206,2.21e+03,0:22
43.7%,218500,437.0000000013585,94.03988967341965,64.1613972967139,158.20128697013354,302.62091022990074,2.21e+03,0:21
43.8%,219000,438.0000000013633,103.60670276347722,83.73998147426654,187.34668423774377,394.96442540342645,2.21e+03,0:21
43.9%,219500,439.00000000136805,113.51086724309451,48.815387635611685,162.3262548787062,230.24057551612648,2.21e+03,0:21
44.0%,220000,440.0000000013728,90.02719510637183,66.90255486445604,156.92974997082786,315.54973711310504,2.21e+03,0:21
44.1%,220500,441.0000000013776,94.30492166278731,55.952485731665526,150.25740739445283,263.9031080236366,2.21e+03,0:21
44.2%,221000,442.0000000013824,99.28609333714053,65.80958191318207,165.09567525032259,310.39466750261,2.22e+03,0:21
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99.5%,497500,994.9999999902951,84.00517640163802,64.65651768895762,148.66169409059563,304.9561739567999,2.24e+03,0:00
99.6%,498000,995.9999999902715,118.56641361994093,67.53867837896166,186.1050919989026,318.55005015317334,2.24e+03,0:00
99.7%,498500,996.9999999902478,120.51405104354778,65.86839799000012,186.3824490335479,310.6720769022295,2.24e+03,0:00
99.8%,499000,997.9999999902242,96.60453181799264,39.57048603609093,136.17501785408356,186.636466894631,2.24e+03,0:00
99.9%,499500,998.9999999902005,102.93132513176653,62.84017058478405,165.7714957165506,296.3892686661228,2.24e+03,0:00
100.0%,500000,999.9999999901769,110.34845004509808,74.99968850072727,185.34813854582535,353.74033230743765,2.24e+03,0:00

In [10]:

    

traj = mdt.load_hdf5("output/sim_1ns.hdf5")

view = ng.show_mdtraj(traj)
view.add_ball_and_stick("all")

view