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Unverified Commit a6cd8c22 authored by Peter Eastman's avatar Peter Eastman Committed by GitHub
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Do not add constraints involving extra particles (#3506) 

* Do not add constraints involving extra particles

* Added test case
parent 4dc111b8
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Showing with 492 additions and 3 deletions
wrappers/python/openmm/app/internal/amber_file_parser.py
View file @ a6cd8c22
...@@ -768,15 +768,18 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No ...@@ -768,15 +768,18 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
# Add constraints. # Add constraints.
isWater = [prmtop.getResidueLabel(i) in ('WAT', 'HOH', 'TP4', 'TP5', 'T4E') for i in range(prmtop.getNumAtoms())] isWater = [prmtop.getResidueLabel(i) in ('WAT', 'HOH', 'TP4', 'TP5', 'T4E') for i in range(prmtop.getNumAtoms())]
isEP = [a.element is None for a in topology.atoms()]
if shake in ('h-bonds', 'all-bonds', 'h-angles'): if shake in ('h-bonds', 'all-bonds', 'h-angles'):
for (iAtom, jAtom, k, rMin) in prmtop.getBondsWithH(): for (iAtom, jAtom, k, rMin) in prmtop.getBondsWithH():
system.addConstraint(iAtom, jAtom, rMin) if not (isEP[iAtom] or isEP[jAtom]):
system.addConstraint(iAtom, jAtom, rMin)
if shake in ('all-bonds', 'h-angles'): if shake in ('all-bonds', 'h-angles'):
for (iAtom, jAtom, k, rMin) in prmtop.getBondsNoH(): for (iAtom, jAtom, k, rMin) in prmtop.getBondsNoH():
system.addConstraint(iAtom, jAtom, rMin) if not (isEP[iAtom] or isEP[jAtom]):
system.addConstraint(iAtom, jAtom, rMin)
if rigidWater and shake is None: if rigidWater and shake is None:
for (iAtom, jAtom, k, rMin) in prmtop.getBondsWithH(): for (iAtom, jAtom, k, rMin) in prmtop.getBondsWithH():
if isWater[iAtom] and isWater[jAtom]: if isWater[iAtom] and isWater[jAtom] and not (isEP[iAtom] or isEP[jAtom]):
system.addConstraint(iAtom, jAtom, rMin) system.addConstraint(iAtom, jAtom, rMin)
# Add harmonic bonds. # Add harmonic bonds.
......
wrappers/python/tests/TestAmberPrmtopFile.py
View file @ a6cd8c22
...@@ -448,5 +448,14 @@ class TestAmberPrmtopFile(unittest.TestCase): ...@@ -448,5 +448,14 @@ class TestAmberPrmtopFile(unittest.TestCase):
OpenMM_CMAP_E = simulation.context.getState(getEnergy=True, groups=1<<i).getPotentialEnergy().value_in_unit(kilojoules_per_mole)/conversion OpenMM_CMAP_E = simulation.context.getState(getEnergy=True, groups=1<<i).getPotentialEnergy().value_in_unit(kilojoules_per_mole)/conversion
self.assertAlmostEqual(OpenMM_CMAP_E, sander_CMAP_E, places=4) self.assertAlmostEqual(OpenMM_CMAP_E, sander_CMAP_E, places=4)
def testEPConstraints(self):
"""Test different types of constraints when using extra particles"""
prmtop = AmberPrmtopFile('systems/peptide_with_tip4p.prmtop')
for constraints in (HBonds, AllBonds):
system = prmtop.createSystem(constraints=constraints)
integrator = VerletIntegrator(0.001*picoseconds)
# If a constraint was added to a massless particle, this will throw an exception.
context = Context(system, integrator, Platform.getPlatformByName('Reference'))
if __name__ == '__main__': if __name__ == '__main__':
unittest.main() unittest.main()
wrappers/python/tests/systems/peptide_with_tip4p.inpcrd 0 → 100644
View file @ a6cd8c22
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wrappers/python/tests/systems/peptide_with_tip4p.prmtop 0 → 100644
View file @ a6cd8c22
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12 54 60 12 54 63 12 48 51 13
42 45 15 78 75 17 81 75 17 81
78 18 90 87 17 93 87 17 93 90
18 102 99 17 105 99 17 105 102 18
114 111 17 117 111 17 117 114 18 126
123 17 129 123 17 129 126 18 138 135
17 141 135 17 141 138 18 150 147 17
153 147 17 153 150 18 162 159 17 165
159 17 165 162 18 174 171 17 177 171
17 177 174 18 186 183 17 189 183 17
189 186 18 198 195 17 201 195 17 201
198 18 210 207 17 213 207 17 213 210
18 222 219 17 225 219 17 225 222 18
234 231 17 237 231 17 237 234 18 246
243 17 249 243 17 249 246 18
%FLAG BONDS_WITHOUT_HYDROGEN
%FORMAT(10I8)
36 39 1 36 42 2 27 30 3 27
33 3 18 27 5 12 18 7 12 36
8 0 12 10 66 69 11 66 72 11
48 54 14 48 66 8 42 48 16 84
75 19 96 87 19 108 99 19 120 111
19 132 123 19 144 135 19 156 147 19
168 159 19 180 171 19 192 183 19 204
195 19 216 207 19 228 219 19 240 231
19 252 243 19
%FLAG ANGLES_INC_HYDROGEN
%FORMAT(10I8)
36 42 45 2 24 18 27 5 21 18
24 6 21 18 27 5 15 12 18 9
15 12 36 10 12 18 21 11 12 18
24 11 9 0 12 15 6 0 9 16
6 0 12 15 3 0 6 16 3 0
9 16 3 0 12 15 0 12 15 17
60 54 63 21 57 54 60 21 57 54
63 21 51 48 54 23 51 48 66 24
48 54 57 25 48 54 60 25 48 54
63 25 45 42 48 27 42 48 51 28
%FLAG ANGLES_WITHOUT_HYDROGEN
%FORMAT(10I8)
39 36 42 1 36 42 48 3 30 27
33 4 18 12 36 7 18 27 30 8
18 27 33 8 12 18 27 12 12 36
39 13 12 36 42 14 0 12 18 18
0 12 36 19 69 66 72 20 54 48
66 22 48 66 69 26 48 66 72 26
42 48 54 29 42 48 66 30
%FLAG DIHEDRALS_INC_HYDROGEN
%FORMAT(10I8)
39 36 42 45 1 39 36 -42 45 2
36 42 48 51 3 24 18 12 36 14
24 18 27 30 3 24 18 27 33 3
21 18 12 36 14 21 18 27 30 3
21 18 27 33 3 15 12 18 21 14
15 12 18 24 14 15 12 18 27 14
15 12 36 39 3 15 12 36 42 3
12 36 42 45 2 9 0 12 15 14
9 0 12 18 14 9 0 12 36 14
6 0 12 15 14 6 0 12 18 14
6 0 12 36 14 3 0 12 15 14
3 0 12 18 14 3 0 12 36 14
0 12 18 21 14 0 12 18 24 14
63 54 48 66 14 60 54 48 66 14
57 54 48 66 14 51 48 54 57 14
51 48 54 60 14 51 48 54 63 14
51 48 66 69 3 51 48 66 72 3
45 42 48 51 3 45 42 48 54 3
45 42 48 66 3 42 48 54 57 14
42 48 54 60 14 42 48 54 63 14
36 48 -42 -45 25
%FLAG DIHEDRALS_WITHOUT_HYDROGEN
%FORMAT(10I8)
39 36 42 48 2 36 42 48 54 1
36 42 -48 54 4 36 42 -48 54 5
36 42 -48 54 6 36 42 48 66 7
36 42 -48 66 8 36 42 -48 66 9
36 42 -48 66 6 27 18 12 36 10
27 18 -12 36 11 27 18 -12 36 12
27 18 -12 36 13 18 12 36 39 3
18 12 36 42 15 18 12 -36 42 16
18 12 -36 42 17 18 12 -36 42 6
12 18 27 30 7 12 18 -27 30 18
12 18 -27 30 19 12 18 -27 30 20
12 18 27 33 7 12 18 -27 33 18
12 18 -27 33 19 12 18 -27 33 20
12 36 42 48 2 0 12 18 27 21
0 12 -18 27 22 0 12 -18 27 12
0 12 -18 27 23 0 12 36 39 3
0 12 36 42 3 54 48 66 69 3
54 48 66 72 3 42 48 66 69 3
42 48 66 72 3 12 42 -36 -39 24
18 30 -27 -33 24 48 69 -66 -72 24
%FLAG EXCLUDED_ATOMS_LIST
%FORMAT(10I8)
2 3 4 5 6 7 8 9 10 13
14 15 3 4 5 6 7 13 4 5
6 7 13 5 6 7 13 6 7 8
9 10 11 12 13 14 15 16 17 7
8 9 10 13 14 15 8 9 10 11
12 13 14 15 9 10 11 12 13 10
11 12 13 11 12 13 12 0 14 15
16 17 18 19 23 15 16 17 16 17
18 19 20 21 22 23 24 25 17 18
19 23 18 19 20 21 22 23 24 25
19 20 21 22 23 24 25 20 21 22
23 24 25 21 22 23 22 23 23 24
25 25 0 27 28 29 28 29 29 0
31 32 33 32 33 33 0 35 36 37
36 37 37 0 39 40 41 40 41 41
0 43 44 45 44 45 45 0 47 48
49 48 49 49 0 51 52 53 52 53
53 0 55 56 57 56 57 57 0 59
60 61 60 61 61 0 63 64 65 64
65 65 0 67 68 69 68 69 69 0
71 72 73 72 73 73 0 75 76 77
76 77 77 0 79 80 81 80 81 81
0 83 84 85 84 85 85 0
%FLAG HBOND_ACOEF
%FORMAT(5E16.8)
0.00000000E+00
%FLAG HBOND_BCOEF
%FORMAT(5E16.8)
0.00000000E+00
%FLAG HBCUT
%FORMAT(5E16.8)
0.00000000E+00
%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
N3 H H H CX HP 2C HC HC CO O2 O2 C O N H CX H1 CT HC
HC HC C O2 O2 OW HW HW EP OW HW HW EP OW HW HW EP OW HW HW
EP OW HW HW EP OW HW HW EP OW HW HW EP OW HW HW EP OW HW HW
EP OW HW HW EP OW HW HW EP OW HW HW EP OW HW HW EP OW HW HW
EP OW HW HW EP
%FLAG TREE_CHAIN_CLASSIFICATION
%FORMAT(20a4)
BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA
BLA BLA BLA BLA BLA M S E E M S E E M S E E M S E
E M S E E M S E E M S E E M S E E M S E
E M S E E M S E E M S E E M S E E M S E
E M S E E
%FLAG JOIN_ARRAY
%FORMAT(10I8)
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0
%FLAG IROTAT
%FORMAT(10I8)
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0
%FLAG SOLVENT_POINTERS
%FORMAT(3I8)
2 16 2
%FLAG ATOMS_PER_MOLECULE
%FORMAT(10I8)
25 4 4 4 4 4 4 4 4 4
4 4 4 4 4 4
%FLAG BOX_DIMENSIONS
%FORMAT(5E16.8)
1.09471219E+02 1.30633205E+01 1.30633205E+01 1.30633205E+01
%FLAG RADIUS_SET
%FORMAT(1a80)
H(N)-modified Bondi radii (mbondi2)
%FLAG RADII
%FORMAT(5E16.8)
1.55000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00
1.20000000E+00 1.70000000E+00 1.20000000E+00 1.20000000E+00 1.70000000E+00
1.50000000E+00 1.50000000E+00 1.70000000E+00 1.50000000E+00 1.55000000E+00
1.30000000E+00 1.70000000E+00 1.20000000E+00 1.70000000E+00 1.20000000E+00
1.20000000E+00 1.20000000E+00 1.70000000E+00 1.50000000E+00 1.50000000E+00
1.50000000E+00 1.20000000E+00 1.20000000E+00 1.50000000E+00 1.50000000E+00
1.20000000E+00 1.20000000E+00 1.50000000E+00 1.50000000E+00 1.20000000E+00
1.20000000E+00 1.50000000E+00 1.50000000E+00 1.20000000E+00 1.20000000E+00
1.50000000E+00 1.50000000E+00 1.20000000E+00 1.20000000E+00 1.50000000E+00
1.50000000E+00 1.20000000E+00 1.20000000E+00 1.50000000E+00 1.50000000E+00
1.20000000E+00 1.20000000E+00 1.50000000E+00 1.50000000E+00 1.20000000E+00
1.20000000E+00 1.50000000E+00 1.50000000E+00 1.20000000E+00 1.20000000E+00
1.50000000E+00 1.50000000E+00 1.20000000E+00 1.20000000E+00 1.50000000E+00
1.50000000E+00 1.20000000E+00 1.20000000E+00 1.50000000E+00 1.50000000E+00
1.20000000E+00 1.20000000E+00 1.50000000E+00 1.50000000E+00 1.20000000E+00
1.20000000E+00 1.50000000E+00 1.50000000E+00 1.20000000E+00 1.20000000E+00
1.50000000E+00 1.50000000E+00 1.20000000E+00 1.20000000E+00 1.50000000E+00
%FLAG SCREEN
%FORMAT(5E16.8)
7.90000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.90000000E-01
8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01
8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01
8.50000000E-01 8.50000000E-01 8.50000000E-01 8.00000000E-01 8.50000000E-01
8.50000000E-01 8.50000000E-01 8.00000000E-01 8.50000000E-01 8.50000000E-01
8.50000000E-01 8.00000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01
8.00000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.00000000E-01
8.50000000E-01 8.50000000E-01 8.50000000E-01 8.00000000E-01 8.50000000E-01
8.50000000E-01 8.50000000E-01 8.00000000E-01 8.50000000E-01 8.50000000E-01
8.50000000E-01 8.00000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01
8.00000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.00000000E-01
8.50000000E-01 8.50000000E-01 8.50000000E-01 8.00000000E-01 8.50000000E-01
8.50000000E-01 8.50000000E-01 8.00000000E-01 8.50000000E-01 8.50000000E-01
8.50000000E-01 8.00000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01
8.00000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.00000000E-01
%FLAG IPOL
%FORMAT(1I8)
0
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