Get potential energy

Get potential energy.

The function molsysmt.molecular_mecanics.potential_energy_minimization() allows us to …

import molsysmt as msm

molecular_system = msm.convert(msm.systems['Barnase-Barstar']['barnase_barstar.h5msm'])

msm.info(molecular_system, element='molecule')

index	name	type	n atoms	n groups	n components	chain index	entity index	entity name
0	BARNASE	protein	1727	110	1	0	0	protein 0
1	BARSTAR	protein	1432	89	1	0	1	protein 1

msm.molecular_mechanics.get_potential_energy(molecular_system)

-25019.433705570038 kilojoule/mole

msm.molecular_mechanics.get_potential_energy(molecular_system, decomposition=True)

{'HarmonicBondForce': <Quantity(410.784811, 'kilojoule / mole')>,
 'NonbondedForce': <Quantity(-36663.969, 'kilojoule / mole')>,
 'PeriodicTorsionForce': <Quantity(9539.07638, 'kilojoule / mole')>,
 'CMMotionRemover': <Quantity(0.0, 'kilojoule / mole')>,
 'HarmonicAngleForce': <Quantity(1694.67414, 'kilojoule / mole')>}

msm.molecular_mechanics.get_potential_energy(molecular_system, selection='molecule_name=="BARNASE"', decomposition=True)

{'HarmonicBondForce': <Quantity(233.452333, 'kilojoule / mole')>,
 'NonbondedForce': <Quantity(-19305.2171, 'kilojoule / mole')>,
 'PeriodicTorsionForce': <Quantity(5109.72271, 'kilojoule / mole')>,
 'CMMotionRemover': <Quantity(0.0, 'kilojoule / mole')>,
 'HarmonicAngleForce': <Quantity(952.452238, 'kilojoule / mole')>}

msm.molecular_mechanics.get_potential_energy(molecular_system, selection='molecule_name=="BARSTAR"', decomposition=True)

{'HarmonicBondForce': <Quantity(177.332478, 'kilojoule / mole')>,
 'NonbondedForce': <Quantity(-14123.1861, 'kilojoule / mole')>,
 'PeriodicTorsionForce': <Quantity(4429.35367, 'kilojoule / mole')>,
 'CMMotionRemover': <Quantity(0.0, 'kilojoule / mole')>,
 'HarmonicAngleForce': <Quantity(742.221902, 'kilojoule / mole')>}