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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
# Add constraints.
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'):
for (iAtom, jAtom, k, rMin) in prmtop.getBondsWithH():
if not (isEP[iAtom] or isEP[jAtom]):
system.addConstraint(iAtom, jAtom, rMin)
if shake in ('all-bonds', 'h-angles'):
for (iAtom, jAtom, k, rMin) in prmtop.getBondsNoH():
if not (isEP[iAtom] or isEP[jAtom]):
system.addConstraint(iAtom, jAtom, rMin)
if rigidWater and shake is None:
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)
# Add harmonic bonds.
......
wrappers/python/tests/TestAmberPrmtopFile.py
View file @ a6cd8c22
......@@ -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
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__':
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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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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