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Commit 3e84be61 authored by Jason Swails's avatar Jason Swails
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Add a test for the previous commit.

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wrappers/python/tests/TestGromacsTopFile.py
View file @ 3e84be61
......@@ -31,6 +31,20 @@ class TestGromacsTopFile(unittest.TestCase):
f.getNonbondedMethod()==methodMap[method]
for f in forces))
def test_ff99SBILDN(self):
""" Test Gromacs topology #define replacement as used in ff99SB-ILDN """
top = GromacsTopFile('systems/aidilnaaaaa.top')
gro = GromacsGroFile('systems/aidilnaaaaa.gro')
system = top.createSystem()
for force in system.getForces():
if isinstance(force, PeriodicTorsionForce):
force.setForceGroup(1)
context = Context(system, VerletIntegrator(1*femtosecond),
Platform.getPlatformByName('Reference'))
context.setPositions(gro.positions)
ene = context.getState(getEnergy=True, groups=2**1).getPotentialEnergy()
self.assertAlmostEqual(ene.value_in_unit(kilojoules_per_mole), 341.6905133582857)
def test_Cutoff(self):
"""Test to make sure the nonbondedCutoff parameter is passed correctly."""
......
wrappers/python/tests/systems/aidilnaaaaa.gro 0 → 100644
View file @ 3e84be61
S C A M O R G
146
1ALA N 1 0.333 0.155 -0.000
1ALA H1 2 0.360 0.104 -0.082
1ALA H2 3 0.360 0.104 0.082
1ALA H3 4 0.233 0.167 0.000
1ALA CA 5 0.397 0.285 -0.000
1ALA HA 6 0.364 0.328 -0.084
1ALA CB 7 0.358 0.365 0.123
1ALA HB1 8 0.403 0.454 0.121
1ALA HB2 9 0.259 0.379 0.124
1ALA HB3 10 0.385 0.316 0.206
1ALA C 11 0.549 0.271 -0.000
1ALA O 12 0.601 0.159 -0.000
2ILE N 13 0.619 0.384 -0.000
2ILE H 14 0.571 0.471 0.000
2ILE CA 15 0.764 0.384 -0.000
2ILE HA 16 0.791 0.337 0.084
2ILE CB 17 0.815 0.312 -0.124
2ILE HB 18 0.781 0.218 -0.124
2ILE CG2 19 0.764 0.384 -0.249
2ILE HG21 20 0.797 0.337 -0.331
2ILE HG22 21 0.664 0.384 -0.249
2ILE HG23 22 0.797 0.478 -0.249
2ILE CG1 23 0.967 0.312 -0.124
2ILE HG11 24 1.001 0.265 -0.043
2ILE HG12 25 1.001 0.406 -0.125
2ILE CD 26 1.018 0.240 -0.249
2ILE HD1 27 1.118 0.240 -0.249
2ILE HD2 28 0.985 0.146 -0.249
2ILE HD3 29 0.985 0.287 -0.331
2ILE C 30 0.819 0.526 -0.000
2ILE O 31 0.743 0.622 0.000
3ASP N 32 0.952 0.539 -0.000
3ASP H 33 1.008 0.456 0.000
3ASP CA 34 1.016 0.668 0.000
3ASP HA 35 0.983 0.711 -0.084
3ASP CB 36 0.977 0.749 0.123
3ASP HB1 37 1.004 0.700 0.206
3ASP HB2 38 0.878 0.763 0.124
3ASP CG 39 1.047 0.885 0.119
3ASP OD1 40 0.986 0.979 0.062
3ASP OD2 41 1.160 0.893 0.174
3ASP C 42 1.168 0.654 -0.000
3ASP O 43 1.220 0.543 -0.000
4ILE N 44 1.238 0.768 -0.000
4ILE H 45 1.190 0.855 0.000
4ILE CA 46 1.383 0.768 -0.000
4ILE HA 47 1.410 0.720 0.084
4ILE CB 48 1.434 0.696 -0.124
4ILE HB 49 1.401 0.602 -0.124
4ILE CG2 50 1.383 0.768 -0.249
4ILE HG21 51 1.416 0.721 -0.331
4ILE HG22 52 1.283 0.768 -0.249
4ILE HG23 53 1.416 0.862 -0.249
4ILE CG1 54 1.586 0.696 -0.124
4ILE HG11 55 1.620 0.649 -0.043
4ILE HG12 56 1.620 0.790 -0.125
4ILE CD 57 1.637 0.624 -0.249
4ILE HD1 58 1.737 0.624 -0.249
4ILE HD2 59 1.604 0.530 -0.249
4ILE HD3 60 1.604 0.671 -0.331
4ILE C 61 1.438 0.910 -0.000
4ILE O 62 1.362 1.006 0.000
5LEU N 63 1.571 0.923 -0.000
5LEU H 64 1.628 0.840 0.000
5LEU CA 65 1.635 1.052 0.000
5LEU HA 66 1.602 1.095 -0.084
5LEU CB 67 1.596 1.133 0.123
5LEU HB1 68 1.623 1.084 0.206
5LEU HB2 69 1.497 1.147 0.124
5LEU CG 70 1.666 1.269 0.119
5LEU HG 71 1.765 1.255 0.119
5LEU CD1 72 1.623 1.344 -0.006
5LEU HD11 73 1.669 1.433 -0.009
5LEU HD12 74 1.649 1.291 -0.087
5LEU HD13 75 1.524 1.357 -0.006
5LEU CD2 76 1.626 1.349 0.243
5LEU HD21 77 1.672 1.438 0.240
5LEU HD22 78 1.527 1.363 0.244
5LEU HD23 79 1.654 1.300 0.325
5LEU C 80 1.787 1.038 -0.000
5LEU O 81 1.839 0.927 -0.000
6ASN N 82 1.857 1.152 -0.000
6ASN H 83 1.809 1.239 0.000
6ASN CA 84 2.002 1.152 -0.000
6ASN HA 85 2.026 1.103 0.084
6ASN CB 86 2.057 1.080 -0.123
6ASN HB1 87 2.025 1.127 -0.205
6ASN HB2 88 2.025 0.986 -0.124
6ASN CG 89 2.209 1.080 -0.123
6ASN OD1 90 2.272 1.133 -0.032
6ASN ND2 91 2.269 1.021 -0.227
6ASN HD21 92 2.214 0.979 -0.299
6ASN HD22 93 2.369 1.018 -0.232
6ASN C 94 2.057 1.294 -0.000
6ASN O 95 1.981 1.390 0.000
7ALA N 96 2.190 1.306 -0.000
7ALA H 97 2.247 1.224 0.000
7ALA CA 98 2.254 1.436 0.000
7ALA HA 99 2.222 1.479 -0.084
7ALA CB 100 2.215 1.517 0.123
7ALA HB1 101 2.261 1.606 0.121
7ALA HB2 102 2.116 1.530 0.124
7ALA HB3 103 2.243 1.468 0.206
7ALA C 104 2.406 1.422 -0.000
7ALA O 105 2.458 1.311 -0.000
8ALA N 106 2.476 1.535 -0.000
8ALA H 107 2.428 1.623 0.000
8ALA CA 108 2.621 1.535 -0.000
8ALA HA 109 2.645 1.487 0.084
8ALA CB 110 2.676 1.464 -0.123
8ALA HB1 111 2.776 1.466 -0.121
8ALA HB2 112 2.644 1.370 -0.124
8ALA HB3 113 2.644 1.511 -0.206
8ALA C 114 2.676 1.677 0.000
8ALA O 115 2.600 1.774 0.000
9ALA N 116 2.809 1.690 -0.000
9ALA H 117 2.866 1.608 -0.000
9ALA CA 118 2.873 1.820 0.000
9ALA HA 119 2.841 1.863 -0.084
9ALA CB 120 2.834 1.901 0.123
9ALA HB1 121 2.880 1.990 0.121
9ALA HB2 122 2.735 1.914 0.124
9ALA HB3 123 2.862 1.851 0.206
9ALA C 124 3.025 1.806 -0.000
9ALA O 125 3.077 1.695 -0.000
10ALA N 126 3.095 1.919 -0.000
10ALA H 127 3.047 2.007 0.000
10ALA CA 128 3.240 1.919 -0.000
10ALA HA 129 3.264 1.871 0.084
10ALA CB 130 3.295 1.848 -0.123
10ALA HB1 131 3.395 1.850 -0.121
10ALA HB2 132 3.263 1.753 -0.124
10ALA HB3 133 3.263 1.895 -0.206
10ALA C 134 3.295 2.061 0.000
10ALA O 135 3.219 2.158 0.000
11ALA N 136 3.428 2.074 -0.000
11ALA H 137 3.485 1.992 -0.000
11ALA CA 138 3.493 2.204 0.000
11ALA HA 139 3.460 2.247 -0.084
11ALA CB 140 3.453 2.285 0.123
11ALA HB1 141 3.499 2.374 0.121
11ALA HB2 142 3.354 2.298 0.124
11ALA HB3 143 3.481 2.235 0.206
11ALA C 144 3.644 2.190 -0.000
11ALA OC1 145 3.716 2.289 -0.000
11ALA OC2 146 3.696 2.079 -0.000
3.48257 2.26962 0.65582
wrappers/python/tests/systems/aidilnaaaaa.top 0 → 100644
View file @ 3e84be61
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