molsysmt.molecular_dynamics package#
Submodules#
molsysmt.molecular_dynamics.md_protocols module#
molsysmt.molecular_dynamics.run_NPT_equilibration module#
- molsysmt.molecular_dynamics.run_NPT_equilibration.run_NPT_equilibration(item, temperature='300 K', pressure='1.0 atm', time='1.0 ns', protocol=0, forcefield=['AMBER99SB-ILDN', 'TIP3P'], engine='OpenMM', verbose=True, form_out=None, *kwargs)[source]#
To be written soon…
Description
- Parameters:
item (molecular model) – Molecular model in any form to be operated by the method.
protocol (int (default 0)) – description.
forcefield (list or str (default ["AMBER99SB-ILDN", "TIP3P"])) – Forcefield to model the inter-atomic interactions.
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 m3t >>> system = m3t.load(‘pdb:1B3T’) >>> minimized_system = m3t.minimze(system) >>> minimized_equilibrated = m3t.equilibration_NPT(system)
molsysmt.molecular_dynamics.run_NVT_equilibration module#
Potential Energy#
Methods related with the potential energy of the system. From energy minimization to potential energy contribution of specific set of atoms or interactions.