parmed.openmm.utils module¶
This package contains some useful functionality for common tasks in OpenMM
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parmed.openmm.utils.energy_decomposition(structure, context, nrg=Unit({BaseUnit(base_dim=BaseDimension('amount'), name='mole', symbol='mol'): - 1.0, ScaledUnit(factor=4.184, master=kilojoule, name='kilocalorie', symbol='kcal'): 1.0}))[source]¶ This computes the energy of every force group in the given structure and computes the energy for each force group for the given Context. Note, the context must have positions already assigned.
- Parameters
- structureStructure
This should be the Structure object from which the System object in the Context was created
- contextmm.Context
The OpenMM context set up for computing forces and energies
- nrgenergy unit, optional
The unit to convert all energies into. Default is kcal/mol
- Returns
- dict {str:float}
A dictionary mapping the name of the force group (taken from the attribute names of the format XXX_FORCE_GROUP in the structure object) with the energy of that group in
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parmed.openmm.utils.energy_decomposition_system(structure, system, platform=None, nrg=Unit({BaseUnit(base_dim=BaseDimension('amount'), name='mole', symbol='mol'): - 1.0, ScaledUnit(factor=4.184, master=kilojoule, name='kilocalorie', symbol='kcal'): 1.0}))[source]¶ This function computes the energy contribution for all of the different force groups.
- Parameters
- structureStructure
The Structure with the coordinates for this system
- systemmm.System
The OpenMM System object to get decomposed energies from
- platformstr
The platform to use. Options are None (default), ‘CPU’, ‘Reference’, ‘CUDA’, and ‘OpenCL’. None will pick default OpenMM platform for this installation and computer
- nrgenergy unit, optional
The unit to convert all energies into. Default is kcal/mol
- Returns
- energieslist of tuple
Each entry is a tuple with the name of the force followed by its contribution