Pin atoms#

Freezing atom positions by setting their masses to zero in OpenMM simulation systems.

The function molsysmt.third_party.openmm.forces.pin_atoms() pins selected atoms in place by modifying their particle masses to zero within the OpenMM System.

Added in version 1.0.0.

API documentation

Follow this link for a detailed description of the input arguments, raised errors, and returned objects: molsysmt.third_party.openmm.forces.pin_atoms().

Basic usage#

Let’s freeze selected atoms by setting mass to zero:

import molsysmt as msm

molsys = msm.convert(msm.systems['Trp-Cage']['1l2y.h5msm'], to_form='molsysmt.MolSys')
force = msm.third_party.openmm.forces.pin_atoms(molsys, selection=[0], force_constant='5000 kJ/(mol*nm**2)', return_force=True)
print('Atoms pinned successfully:', type(force))

Atoms pinned successfully: <class 'openmm.openmm.CustomExternalForce'>