molsysmt.molecular_mechanics.potential_energy_minimization#

molsysmt.molecular_mechanics.potential_energy_minimization(molecular_system, method='L-BFGS', platform='CPU', engine='OpenMM', to_form=None, in_place=False, verbose=False)[source]#

To be written soon…

potential_energy_minimization(molecular_system, …)

A new structure is returned with the molecular model relaxed to the nearest potential energy local minimum.

Parameters:

  • item (molecular model) – Molecular model in any form to be operated by the method.

  • method (str (default "AMBER99SB-ILDN")) – Energy minimization method.

  • method – Forcefield to model the inter-atomic interactions.

  • selection (str, int, list, tuple or numpy array (default None)) – Region to be minimized defined as a selection sentence or atoms indices list. By default None means all atoms and there by the whole molecular model is minized.

  • syntax (str (default "mdtraj")) – Name of the selection syntax used: “mdtraj” or “amber”.

  • engine (str (default "openmm"))

Returns:

item – The result is a new molecular model with coordinates or positions relaxed to the nearest local minimum of the potential energy.

Return type:

molecular model

Examples

Remove chains 0 and 1 from the pdb: 1B3T. >>> import molsysmt as msm >>> system = msm.load(‘pdb:1B3T’) Check the number of chains >>> minimized_system = m3t.molecular_mechanics.potential_energy_minimization(system)