Get degrees of freedom#

Calculating mechanical degrees of freedom for parameterized molecular systems.

The function molsysmt.molecular_mechanics.get_degrees_of_freedom() computes the effective number of mechanical degrees of freedom (\(3 N_{\text{particles}} - N_{\text{constraints}}\)) accounting for force field constraints.

Added in version 1.0.0.

API documentation

Follow this link for a detailed description of the input arguments, raised errors, and returned objects of this function: molsysmt.molecular_mechanics.get_degrees_of_freedom().

Note

Molecular Mechanics Backend Engine

Molecular mechanics and force evaluations in MolSysMT are executed using backend simulation engines (currently OpenMM by default). MolSysMT intentionally unifies the Pythonic interface and data structures while delegating energy evaluations, parameterizations, and gradient calculations to high-performance, battle-tested molecular simulation engines.

Basic usage#

Let’s determine the mechanical degrees of freedom for a parameterized molecular system:

import molsysmt as msm

prmtop_sys = msm.convert(msm.systems['pentalanine']['pentalanine.prmtop'])
omm_sys = msm.convert(prmtop_sys, to_form='openmm.System')

Note

Demo Systems Catalog

This tutorial uses demonstration datasets provided by MolSysMT. To explore the full catalog of bundled systems, forms, and file paths, visit the Demo Systems guide.

We calculate the degrees of freedom directly from the openmm.System object:

dof = msm.molecular_mechanics.get_degrees_of_freedom(omm_sys)
print('Total mechanical degrees of freedom:', dof)

Total mechanical degrees of freedom: 10444

Direct calculation from molecular topologies#

When providing molecular topologies or native MolSysMT objects, the system is automatically converted and parameterized using the specified force field to determine the number of constraints:

molsys = msm.build.build_peptide('AceAlaCysAspGluPheNme')
dof_peptide = msm.molecular_mechanics.get_degrees_of_freedom(molsys, forcefield='AMBER14')
print('Peptide degrees of freedom (AMBER14):', dof_peptide)

Peptide degrees of freedom (AMBER14): 204