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Commit 534fd404 authored by Peter Eastman's avatar Peter Eastman
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Added examples for app

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5.0594938 10.3800678 8.2060242 12.2550905 4.2555296 7.8707021
11.9126701 4.4309631 8.7471741 12.7958441 5.0187957 7.6676172
3.3182484 11.9942641 10.4541850 4.1031209 12.5421488 10.4596007
2.8062236 12.3166513 9.7124779 14.9403059 13.5199690 7.9434615
14.1420293 13.8731015 8.3362508 14.9914014 13.9408267 7.0852655
14.5876753 2.7960026 8.0582267 13.6647761 3.0458105 8.1039053
14.9372995 3.0118328 8.9227563 12.1774852 14.2055249 7.9388714
12.3072231 13.6340761 7.1820056 11.2430060 14.1359162 8.1341529
14.5651269 10.7467616 5.1479954 14.2486548 10.1617455 4.4596392
15.5169487 10.7428825 5.0467467 12.5681496 9.8788732 9.6948028
13.3165312 10.0931549 9.1378099 12.9447305 9.7603750 10.5667984
9.0156239 7.6121730 3.6681548 8.1917518 7.8311336 3.2328123
9.6161205 8.3114833 3.4100825 15.6540823 9.0311038 9.8202854
15.4602695 9.6707243 9.1350448 16.5942717 9.1229677 9.9746811
12.8155637 8.9916319 3.5936639 12.0444071 9.2101187 3.0703923
12.4624598 8.7393844 4.4468465 11.1924636 4.8015800 10.4373348
11.1904335 5.7410860 10.6205177 10.2729273 4.5432872 10.5003345
6.2454498 7.2838616 2.4679561 5.9709626 6.4133132 2.1798013
5.8472854 7.3866475 3.3323240 5.8068472 11.4652765 6.8836099
5.4372787 11.0537374 6.1024016 6.7472053 11.2980938 6.8202925
1.5903418 5.5463874 8.0745435 2.2379220 6.2122160 8.3059394
0.9982453 5.5167574 8.8260591 12.8146625 14.1429222 11.6106606
13.4969723 14.8020816 11.7379153 12.1115887 14.6100211 11.1592889
3.3091152 11.2495160 13.0189741 2.8846872 10.3975058 13.1198263
3.1491229 11.4902854 12.1064699 8.9424539 11.7507279 4.0372929
9.4525206 12.5544059 4.1381115 8.7806976 11.4557099 4.9334133
4.6193030 13.4329820 14.3189001 4.6661255 14.0511584 13.5895872
4.1349128 12.6854324 13.9685190 9.0632844 15.1627636 12.6602221
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3.8071257 13.9555097 4.7656968 3.3645624 13.1205153 4.9178618
3.5091007 14.5182681 5.4803413 10.4755545 13.9738297 4.5887828
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11.8359399 2.2705801 12.4611723 12.0843244 3.4511256 11.5470588
9.3910205 5.5444539 13.2992280 9.3150038 4.6124157 13.0948794
10.2848887 5.6458247 13.6262703 1.9309273 4.3498123 5.7749116
1.8980187 4.8940012 6.5616816 1.2902501 3.6570922 5.9358561
8.1352240 5.0256371 3.8487068 8.6331028 5.7701695 3.5110384
7.5102508 4.8202887 3.1533846 5.2862072 7.0728385 14.2537415
4.7734267 6.2900710 14.4551468 6.1969328 6.7922419 14.3436086
9.9940389 3.8460085 6.4078021 10.0446236 3.1829548 5.7193017
10.8594108 3.8332003 6.8167013 7.9387468 3.6221394 15.5874312
8.3003527 3.4751719 16.4614296 7.8855813 4.5744932 15.5072582
6.5432078 6.3675535 9.0754020 6.4071369 6.0346109 9.9624568
6.9026721 5.6232202 8.5927165 6.2927896 4.9479905 5.8104759
6.9729239 4.8559773 5.1432556 6.6580129 4.5207781 6.5852880
3.6837226 7.3043740 8.6347276 4.5580330 6.9587284 8.4548867
3.7803346 8.2533669 8.5552931 3.9457598 6.6183901 11.2000620
4.5942980 7.3015350 11.3701868 3.6792812 6.7619163 10.2919745
14.6117246 10.7448816 7.9326665 14.5564604 10.6677389 6.9801819
14.8064196 11.6692436 8.0872029 8.4540653 9.3833119 13.1341803
8.3611566 8.7365741 12.4346590 7.5628930 9.6948546 13.2922482
4.8848903 10.1042879 4.7417286 5.4330409 10.3789759 4.0066707
5.0647777 9.1691154 4.8382995 2.9533949 8.5791105 13.8096857
2.3701259 7.8808689 13.5122156 3.8133654 8.1631905 13.8704634
9.1747022 12.0154631 13.8436067 8.9591640 11.1403370 13.5212266
8.4735149 12.2225475 14.4614136 14.0734065 9.2539656 12.0210719
14.7122538 9.0062416 11.3526869 14.2364097 10.1845431 12.1749771
11.2193215 10.4899669 7.3087865 11.4850152 9.7215861 6.8035835
11.5098214 10.3019929 8.2012594 6.5613741 11.4296377 2.8531700
7.3761773 11.7603517 3.2312641 6.0581720 12.2163367 2.6431119
7.6112151 9.3064040 1.4692697 7.1468955 10.0829256 1.7817655
7.0402038 8.5750693 1.7044874 8.4395105 13.2007670 10.7524335
8.5154772 13.7944281 11.4994454 9.1873091 12.6095951 10.8392966
10.9823227 12.0867276 10.6910336 11.3482428 11.2815368 10.3249693
11.7461360 12.5919437 10.9695625 11.6588795 13.0144548 13.8778114
11.8649566 13.5315990 13.0991423 10.7892561 12.6546359 13.7031198
7.0709276 12.3214674 15.4972446 6.7221689 11.4674473 15.7526827
6.3990068 12.6934314 14.9259329 8.5184914 3.7946579 10.7337666
8.7840170 3.2712960 11.4899552 7.6462001 4.1172773 10.9601676
4.2825392 3.9850882 4.2280355 3.4190124 4.1306540 4.6145123
4.8984498 4.2480856 4.9119347 6.0303652 4.7529408 11.3351083
5.2377522 5.2895170 11.3260055 5.9202319 4.1758090 12.0907676
6.0674644 15.0887418 3.7791651 5.9484190 15.4704523 2.9094771
5.2557987 14.6085930 3.9431408 11.8473530 8.1054550 6.0199249
11.0905206 7.5199366 6.0445380 12.5730276 7.5726831 6.3451678
15.3320920 15.3820765 5.5547917 15.7136273 16.2334716 5.7687724
16.0792387 14.7842658 5.5297863 3.3844343 15.2567947 7.1752334
4.2976260 14.9954498 7.2936022 3.3714777 16.1883211 7.3950601
10.8122754 10.0434005 16.6299021 9.9537539 9.6414864 16.4970958
11.3373327 9.3565202 17.0406854 9.8703730 14.6032166 15.4123402
10.2867317 13.7704647 15.1900756 10.6006396 15.1988065 15.5803132
5.7417810 10.0712299 13.2797194 4.9602693 10.6155705 13.1839836
5.7146633 9.4789600 12.5282454 12.5181890 10.5174339 14.5666087
12.4647820 11.4233422 14.2621255 11.8803680 10.4660285 15.2784896
1.8101747 6.1459291 12.8319836 1.0636389 5.9769607 12.2572100
2.5564596 6.2261605 12.2379696 11.0021389 8.6268854 13.2453644
11.5814853 9.3341595 13.5288322 10.1218724 8.9967787 13.3127534
11.8682802 6.2363446 14.2056823 12.6452935 6.1537689 13.6528134
11.5696907 7.1350658 14.0664816 5.8886832 8.5002726 11.0059702
6.6831070 8.0012631 10.8159375 5.6620461 8.9157444 10.1739538
8.4693497 7.3696530 11.2213445 8.5316288 6.6707975 11.8724620
9.3536741 7.4419045 10.8622050 11.1640489 7.5788778 10.6863296
11.5557837 8.2728833 10.1561117 11.2310505 7.8982133 11.5862012
4.6901396 15.1967168 12.1271992 4.3188354 15.9278047 11.6333628
4.9839699 14.5796645 11.4570189 5.6721759 3.4050620 13.7314487
6.2834132 3.2134539 14.4427204 4.9437326 3.8573313 14.1569531
9.1712379 2.7755097 13.1817412 8.5844582 2.7757421 13.9379954
9.6455717 1.9466574 13.2468796 6.8717849 16.5869033 13.1133735
6.8127477 17.0754158 13.9344108 6.0138750 16.1730719 13.0186796
2.6282942 11.5804017 5.6136054 3.3312011 10.9447670 5.4789841
1.9615513 11.3400304 4.9702495 17.3618054 10.6205618 5.3281873
17.5082123 9.6888274 5.4914886 17.7512753 10.7770431 4.4679207
14.1839230 11.9010520 11.3274992 13.7799835 12.7483869 11.5148163
14.9709213 12.1163118 10.8269703 15.3464472 7.8010243 3.5677883
15.1633787 6.9342136 3.9302194 14.4906533 8.2274306 3.5227698
13.9886892 6.4834833 12.4034774 14.0364182 6.4278495 11.4490891
14.0567136 7.4193567 12.5925422 13.8052928 6.4680785 6.8983054
13.8777184 6.0986030 6.0182631 14.7007775 6.7157292 7.1285397
14.4258916 6.5736121 9.7390115 13.7788093 6.6493982 9.0377462
14.9980402 7.3316991 9.6199220 14.5839202 5.3325331 4.5345792
15.1618469 4.7184604 4.9875125 14.1270900 4.7973126 3.8856745
15.9801018 3.5917988 5.9395319 15.4615450 3.1244871 6.5944743
16.8408680 3.6957017 6.3451409 14.0143287 15.7570219 3.2631442
14.4469202 15.4764736 4.0696114 13.2163525 15.2298641 3.2235190
5.6541497 13.5876250 10.2330947 5.7041156 13.8395810 9.3110031
6.5529621 13.3561790 10.4671896 16.9233179 15.1787674 10.5873466
16.0732257 15.4521930 10.9320390 16.9582701 14.2370856 10.7554138
13.6190081 16.4124358 9.0213901 13.6021018 17.0304739 8.2906544
13.0399072 15.7013500 8.7471086 5.9406340 14.1042483 7.5803804
5.6936806 13.1997681 7.3876059 6.6402918 14.2995477 6.9570273
9.3025899 14.3486202 8.2730830 8.7823510 14.1396868 7.4972415
8.9164972 13.8184214 8.9702582 7.6833671 15.6052935 16.7912769
8.2927579 15.0117576 16.3524270 7.8554428 16.4601362 16.3964772
16.2024868 15.7253480 1.5376477 15.9622931 15.7665789 0.6119916
15.3705812 15.8032441 2.0046569
32.8528630 32.8616480 31.8550980 90.0000000 90.0000000 90.0000000
examples/input.pdb 0 → 100644
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examples/input.prmtop 0 → 100644
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examples/simulateAmber.py 0 → 100644
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from simtk.openmm.app import *
from simtk.openmm import *
from simtk.unit import *
prmtop = AmberPrmtopFile('input.prmtop')
inpcrd = AmberInpcrdFile('input.inpcrd')
system = prmtop.createSystem(nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds)
integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
simulation = Simulation(prmtop.topology, system, integrator)
simulation.context.setPositions(inpcrd.positions)
simulation.minimizeEnergy()
simulation.reporters.append(PDBReporter('output.pdb', 1000))
simulation.step(100000)
examples/simulatePdb.py 0 → 100644
View file @ 534fd404
from simtk.openmm.app import *
from simtk.openmm import *
from simtk.unit import *
pdb = PDBFile('input.pdb')
forcefield = ForceField('amber99sb.xml', 'tip3p.xml')
system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds)
integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
simulation = Simulation(pdb.topology, system, integrator)
simulation.context.setPositions(pdb.positions)
simulation.minimizeEnergy()
simulation.reporters.append(PDBReporter('output.pdb', 1000))
simulation.step(100000)
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