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Unverified Commit 0993868a authored by Peter Eastman's avatar Peter Eastman Committed by GitHub
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NBFIX is applied correctly to 1-4 interactions (#3324)

parent 892839b8
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Showing with 6043 additions and 2 deletions
wrappers/python/openmm/app/charmmpsffile.py
View file @ 0993868a
...@@ -1387,6 +1387,11 @@ class CharmmPsfFile(object): ...@@ -1387,6 +1387,11 @@ class CharmmPsfFile(object):
atom1 = self.atom_list[ia1] atom1 = self.atom_list[ia1]
atom4 = self.atom_list[ia4] atom4 = self.atom_list[ia4]
charge_prod = (atom1.charge * atom4.charge) * params.e14fac charge_prod = (atom1.charge * atom4.charge) * params.e14fac
try:
rij, wdij, rij14, wdij14 = atom1.type.nbfix[atom4.type.name]
epsilon = wdij14*ene_conv
sigma = rij14*length_conv*sigma_scale
except KeyError:
epsilon = sqrt(abs(atom1.type.epsilon_14 * atom4.type.epsilon_14)) * ene_conv epsilon = sqrt(abs(atom1.type.epsilon_14 * atom4.type.epsilon_14)) * ene_conv
sigma = (atom1.type.rmin_14 + atom4.type.rmin_14) * (length_conv * sigma_scale) sigma = (atom1.type.rmin_14 + atom4.type.rmin_14) * (length_conv * sigma_scale)
force.addException(ia1, ia4, charge_prod, sigma, epsilon) force.addException(ia1, ia4, charge_prod, sigma, epsilon)
......
wrappers/python/tests/TestCharmmFiles.py
View file @ 0993868a
...@@ -150,6 +150,30 @@ class TestCharmmFiles(unittest.TestCase): ...@@ -150,6 +150,30 @@ class TestCharmmFiles(unittest.TestCase):
ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole) ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
self.assertAlmostEqual(ene, 15559.71602, delta=0.05) self.assertAlmostEqual(ene, 15559.71602, delta=0.05)
def test_NBFIX14(self):
"""Tests CHARMM systems with NBFIX modifications to 1-4 interactions"""
warnings.filterwarnings('ignore', category=CharmmPSFWarning)
psf = CharmmPsfFile('systems/chl1.psf')
crd = CharmmCrdFile('systems/chl1.crd')
params = CharmmParameterSet('systems/par_all36_lipid.prm', 'systems/par_all36_cgenff.prm', 'systems/toppar_all36_lipid_cholesterol.str')
# Turn off charges so we only test the Lennard-Jones energies
for a in psf.atom_list:
a.charge = 0.0
# Compute the Lennard-Jones energy
system = psf.createSystem(params, nonbondedMethod=CutoffNonPeriodic, nonbondedCutoff=12*angstroms)
for i, f in enumerate(system.getForces()):
if isinstance(f, NonbondedForce) or isinstance(f, CustomNonbondedForce):
f.setForceGroup(1)
else:
f.setForceGroup(0)
context = Context(system, VerletIntegrator(2*femtoseconds), Platform.getPlatformByName('Reference'))
context.setPositions(crd.positions)
state = context.getState(getEnergy=True, groups={1})
energy = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
self.assertAlmostEqual(energy, 3.1166, delta=1e-4)
def test_NBThole(self): def test_NBThole(self):
"""Tests CHARMM system with NBTHole""" """Tests CHARMM system with NBTHole"""
warnings.filterwarnings('ignore', category=CharmmPSFWarning) warnings.filterwarnings('ignore', category=CharmmPSFWarning)
......
wrappers/python/tests/systems/chl1.crd 0 → 100644
View file @ 0993868a
* GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V2.0 ON APR, 20. 2017. JOB
* GET A DIFFERENT CONFORMATION FOR LIPIDS PENETRATING PROTEIN / CHOL
* DATE: 9/22/21 15:13: 3 CREATED BY USER: jlee
*
74 EXT
1 1 CHL1 C3 2.0758430000 1.4287490000 -0.0024380000 CHL1 1 0.0000000000
2 1 CHL1 H3 1.7789920000 1.9075100000 -0.9655430000 CHL1 1 0.0000000000
3 1 CHL1 O3 3.4901020000 1.4114150000 0.0741910000 CHL1 1 0.0000000000
4 1 CHL1 H3' 3.6956580000 0.9624930000 0.8967140000 CHL1 1 0.0000000000
5 1 CHL1 C4 1.5114820000 2.2413810000 1.1750860000 CHL1 1 0.0000000000
6 1 CHL1 H4A 1.9148670000 3.2768030000 1.0908510000 CHL1 1 0.0000000000
7 1 CHL1 H4B 1.9116520000 1.8253500000 2.1234900000 CHL1 1 0.0000000000
8 1 CHL1 C5 -0.0042430000 2.2232410000 1.2047520000 CHL1 1 0.0000000000
9 1 CHL1 C6 -0.7185500000 3.3605640000 1.1867230000 CHL1 1 0.0000000000
10 1 CHL1 H6 -0.1961740000 4.3287470000 1.1811170000 CHL1 1 0.0000000000
11 1 CHL1 C7 -2.2182720000 3.4093590000 1.2529030000 CHL1 1 0.0000000000
12 1 CHL1 H7A -2.6174250000 3.6976270000 0.2559360000 CHL1 1 0.0000000000
13 1 CHL1 H7B -2.5510300000 4.1816550000 1.9801080000 CHL1 1 0.0000000000
14 1 CHL1 C8 -2.8493790000 2.0493740000 1.6586470000 CHL1 1 0.0000000000
15 1 CHL1 H8 -2.6976970000 1.9177710000 2.7522240000 CHL1 1 0.0000000000
16 1 CHL1 C14 -4.3402020000 2.0530670000 1.3479140000 CHL1 1 0.0000000000
17 1 CHL1 H14 -4.4174730000 2.1586370000 0.2344860000 CHL1 1 0.0000000000
18 1 CHL1 C15 -5.1864690000 3.2052640000 1.9147900000 CHL1 1 0.0000000000
19 1 CHL1 H15A -5.0243010000 4.1528850000 1.3633690000 CHL1 1 0.0000000000
20 1 CHL1 H15B -4.9339520000 3.3605530000 2.9859010000 CHL1 1 0.0000000000
21 1 CHL1 C16 -6.6269070000 2.6905440000 1.7787000000 CHL1 1 0.0000000000
22 1 CHL1 H16A -7.1958500000 3.2680330000 1.0215770000 CHL1 1 0.0000000000
23 1 CHL1 H16B -7.1376360000 2.7834600000 2.7609420000 CHL1 1 0.0000000000
24 1 CHL1 C17 -6.5372270000 1.1878570000 1.3493380000 CHL1 1 0.0000000000
25 1 CHL1 H17 -6.6019490000 1.1763380000 0.2350740000 CHL1 1 0.0000000000
26 1 CHL1 C13 -5.0880620000 0.7643510000 1.6898470000 CHL1 1 0.0000000000
27 1 CHL1 C18 -5.0064860000 0.4701080000 3.2112890000 CHL1 1 0.0000000000
28 1 CHL1 H18A -5.4771980000 1.2760610000 3.8078890000 CHL1 1 0.0000000000
29 1 CHL1 H18B -3.9571470000 0.3656950000 3.5470390000 CHL1 1 0.0000000000
30 1 CHL1 H18C -5.5253140000 -0.4812360000 3.4456420000 CHL1 1 0.0000000000
31 1 CHL1 C12 -4.4501040000 -0.3574190000 0.8429720000 CHL1 1 0.0000000000
32 1 CHL1 H12A -4.6174580000 -0.1329160000 -0.2328530000 CHL1 1 0.0000000000
33 1 CHL1 H12B -4.9071470000 -1.3405780000 1.0619880000 CHL1 1 0.0000000000
34 1 CHL1 C11 -2.9326770000 -0.4609040000 1.1008090000 CHL1 1 0.0000000000
35 1 CHL1 H11A -2.5100440000 -1.2251340000 0.4155920000 CHL1 1 0.0000000000
36 1 CHL1 H11B -2.8003630000 -0.8324760000 2.1373400000 CHL1 1 0.0000000000
37 1 CHL1 C9 -2.1768110000 0.8895300000 0.9143010000 CHL1 1 0.0000000000
38 1 CHL1 H9 -2.2977970000 1.1402610000 -0.1695780000 CHL1 1 0.0000000000
39 1 CHL1 C10 -0.6446230000 0.8183080000 1.1682710000 CHL1 1 0.0000000000
40 1 CHL1 C19 -0.3877040000 0.1475000000 2.5441910000 CHL1 1 0.0000000000
41 1 CHL1 H19A -0.9335740000 0.6777980000 3.3513270000 CHL1 1 0.0000000000
42 1 CHL1 H19B 0.6897940000 0.1400840000 2.8025550000 CHL1 1 0.0000000000
43 1 CHL1 H19C -0.7162580000 -0.9108240000 2.5315180000 CHL1 1 0.0000000000
44 1 CHL1 C1 0.0140190000 -0.0227780000 0.0327100000 CHL1 1 0.0000000000
45 1 CHL1 H1A -0.3316670000 0.3767310000 -0.9472730000 CHL1 1 0.0000000000
46 1 CHL1 H1B -0.3334130000 -1.0747520000 0.1067690000 CHL1 1 0.0000000000
47 1 CHL1 C2 1.5521950000 -0.0100270000 0.0330650000 CHL1 1 0.0000000000
48 1 CHL1 H2A 1.9243040000 -0.5230830000 0.9458070000 CHL1 1 0.0000000000
49 1 CHL1 H2B 1.9346080000 -0.5653680000 -0.8513700000 CHL1 1 0.0000000000
50 1 CHL1 C20 -7.7246780000 0.3593490000 1.8737490000 CHL1 1 0.0000000000
51 1 CHL1 H20 -7.7090080000 0.3716970000 2.9880740000 CHL1 1 0.0000000000
52 1 CHL1 C21 -7.6153060000 -1.1076400000 1.4054310000 CHL1 1 0.0000000000
53 1 CHL1 H21A -6.7567890000 -1.6098270000 1.8911100000 CHL1 1 0.0000000000
54 1 CHL1 H21B -7.4954750000 -1.1568730000 0.3031920000 CHL1 1 0.0000000000
55 1 CHL1 H21C -8.5172290000 -1.6860490000 1.6875930000 CHL1 1 0.0000000000
56 1 CHL1 C22 -9.0849100000 0.9697470000 1.4326760000 CHL1 1 0.0000000000
57 1 CHL1 H22A -9.1561990000 0.9304830000 0.3238230000 CHL1 1 0.0000000000
58 1 CHL1 H22B -9.1287420000 2.0387760000 1.7346150000 CHL1 1 0.0000000000
59 1 CHL1 C23 -10.3258450000 0.2922230000 2.0422060000 CHL1 1 0.0000000000
60 1 CHL1 H23A -10.2114010000 0.2526360000 3.1483210000 CHL1 1 0.0000000000
61 1 CHL1 H23B -10.4034320000 -0.7498490000 1.6668930000 CHL1 1 0.0000000000
62 1 CHL1 C24 -11.6240990000 1.0427750000 1.7005560000 CHL1 1 0.0000000000
63 1 CHL1 H24A -11.7579260000 1.0650290000 0.5968610000 CHL1 1 0.0000000000
64 1 CHL1 H24B -11.5215770000 2.0951660000 2.0485660000 CHL1 1 0.0000000000
65 1 CHL1 C25 -12.8929290000 0.4444570000 2.3453720000 CHL1 1 0.0000000000
66 1 CHL1 H25 -12.7160890000 0.3730380000 3.4453480000 CHL1 1 0.0000000000
67 1 CHL1 C26 -14.0995530000 1.3709480000 2.1214960000 CHL1 1 0.0000000000
68 1 CHL1 H26A -14.3073370000 1.4755350000 1.0355250000 CHL1 1 0.0000000000
69 1 CHL1 H26B -13.8988040000 2.3788300000 2.5421330000 CHL1 1 0.0000000000
70 1 CHL1 H26C -15.0033380000 0.9555930000 2.6153310000 CHL1 1 0.0000000000
71 1 CHL1 C27 -13.2063260000 -0.9657240000 1.8173800000 CHL1 1 0.0000000000
72 1 CHL1 H27A -12.3832270000 -1.6705450000 2.0552520000 CHL1 1 0.0000000000
73 1 CHL1 H27B -13.3457700000 -0.9412980000 0.7159300000 CHL1 1 0.0000000000
74 1 CHL1 H27C -14.1385570000 -1.3514600000 2.2815630000 CHL1 1 0.0000000000
wrappers/python/tests/systems/chl1.psf 0 → 100644
View file @ 0993868a
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wrappers/python/tests/systems/par_all36_lipid.prm 0 → 100644
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