total_nrg = solute_intraclj.components().total() + solute_intraff.components().total() +\
solventff.components().total() + solute_solventff.components().total() +\
protein_intraclj.components().total() + protein_intraff.components().total() + \
solute_proteinff.components().total() + protein_solventff.components().total()
e_total = system.totalComponent()
system.setComponent( e_total, total_nrg )
# Add a space wrapper that wraps all molecules into the box centered at (0,0,0)
#system.add( SpaceWrapper(Vector(0,0,0), all) )
print("\nTotal energy ")
print(system.energy())
print("Components energies ")
for component in list(system.energyComponents().keys()):
print(component, system.energyComponents().value(component) * kcal_per_mol)
# Note that tip3p water are likely to have bonds between hydrogen atoms.
PDB().write(all, "out.pdb")
print("The AMBER11/sander energies for this system are ")
print("""
# NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
# Etot = -47010.2216 EKtot = 0.0000 EPtot = -47010.2216
# BOND = 898.1982 ANGLE = 5310.2620 DIHED = 2922.5644
# 1-4 NB = 790.8755 1-4 EEL = 7702.0145 VDWAALS = 7345.0484
# EELEC = -71979.1846 EHBOND = 0.0000 RESTRAINT = 0.0000
# EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 1856243.3813
""")
def test_nrg(verbose=False):
top_file = "../io/ose.top"
crd_file = "../io/ose.crd"
amber = Amber()
molecules, space = amber.readCrdTop(crd_file, top_file)
# Overload, we want to calc the energy in a non periodic box for comparison with Sander
space = Cartesian()
moleculeNumbers = molecules.molNums()
moleculeList = []
for moleculeNumber in moleculeNumbers:
molecule = molecules.molecule(moleculeNumber).molecule()
moleculeList.append(molecule)
system = System()
solute = MoleculeGroup("solute", moleculeList[0])
# Add these groups to the System
system.add(solute)
# Now solute bond, angle, dihedral energy
solute_intraff = InternalFF("solute_intraff")
solute_intraff.add(solute)
# Now solute intramolecular CLJ energy
solute_intraclj = IntraCLJFF("solute_intraclj")
solute_intraclj.add(solute)
# Here is the list of all forcefields
forcefields = [solute_intraff, solute_intraclj]
# Add these forcefields to the system
for forcefield in forcefields:
system.add(forcefield)
system.setProperty("space", space)
system.setProperty(
"switchingFunction",
HarmonicSwitchingFunction(coulomb_cutoff, coulomb_feather, lj_cutoff,
lj_feather))
system.setProperty("combiningRules", VariantProperty(combining_rules))
total_nrg = solute_intraclj.components().total(
) + solute_intraff.components().total()
e_total = system.totalComponent()
system.setComponent(e_total, total_nrg)
if verbose:
print("\nTotal energy ")
print(system.energy())
print("Components energies ")
for component in list(system.energyComponents().keys()):
print(component,
system.energyComponents().value(component) * kcal_per_mol)
print("The AMBER14/sander energies for this system are ")
print("""
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -3.4880E+01 1.3388E+01 6.2845E+01 C2 20
BOND = 5.1844 ANGLE = 10.0783 DIHED = 20.1271
VDWAALS = -1.7278 EEL = -256.9757 HBOND = 0.0000
1-4 VDW = 10.6377 1-4 EEL = 177.7958 RESTRAINT = 0.0000
""")
diff = abs(-34.880 - system.energy().value())
print("Difference = %s" % diff)
e_bond = system.energy(solute_intraff.components().bond()).value()
e_ang = system.energy(solute_intraff.components().angle()).value()
e_dih = system.energy( solute_intraff.components().dihedral() ).value() + \
system.energy( solute_intraff.components().improper() ).value()
assert_almost_equal(e_bond, 5.1844, 2)
assert_almost_equal(e_ang, 10.0783, 2)
assert_almost_equal(e_dih, 20.1271, 2)
e_coul = system.energy(solute_intraclj.components().coulomb()).value()
e_lj = system.energy(solute_intraclj.components().lj()).value()
assert_almost_equal(e_coul, -256.9757 + 177.7958, 2)
assert_almost_equal(e_lj, -1.7278 + 10.6377, 2)
assert_almost_equal(system.energy().value(), -34.880, 2)