Transcript Document
Main Objectives To create a flexible, extensible and reusable molecular modeling environment. • Construction of a library for molecular modeling using a common data model and implemented in C for efficiency. • Flexibility is achieved through the combination of a modular underlying library and a high level scripting language. • Development of the interface between the molecular modeling library and the high level scripting language is facilitated by software tools (SWIG) which allow for rapid prototyping. API Hierarchy GUI Scripting Language Intuitive graphical user interface for easy configuration of molecular modeling parameters. Flexible scripting language to drive the underlying C library. Interface Wrapped C structures and functions provide interface to high level scripting language. C Library Molecular modeling C library. C Library Functionality • Molecular model: - stretching: Harmonic, Morse - bending: Harmonic, q-harmonic, cross stretch-bending - torsion: Fourier, cross bend-bend, stretch-stretch - inversion: Umbrella and improper torsions - van der Waals: LJ, exp-6, Morse, WCA - Hydrogen-bonding • Methods: - Short-range nonbonded vdw/Coulombic/H-bonding with an all pair search, cell lists, neighbor lists. - Long-range Coulombic with Ewald, PME. - Integrator: Velocity-verlet, Multiple time steps - Thermostat: Berendsen, Nose-Hoover - Barostat: Berendsen Library to Scripting Language Mapping C structures atom_properties Python objects SWIG ff_properties . . . ff_properties . . . C functions compute_tot_forces() compute_thermo() . . . atom_properties Python functions SWIG compute_tot_forces() compute_thermo() . . . Forces Class Diagram Force ForceBond ForceStretch ForceBend ForceTors ForceNonBond ForceInv ForceShort ForceVdwShort ForceCoulShort Python script to add force contributions to model # Initialize and add force contributions forceStretch = ForceStretch(model) model.add_force(forceStretch) forceBend = ForceBend(model) model.add_force(forceBend) forceTors = ForceTors(model) model.add_force(forceTors) forceCoulShort = ForceCoulShort(model, coul_short_method) model.add_force(forceCoulShort) forceCoulLong = ForceCoulLong(model, coul_long_method) model.add_force(forceCoulLong) # Iterate over force contributions to calculate total force. for force in self.force_list: force.compute_force() ForceLong ForceVdwLong ForceCoulLong MD Script parameters = setup_parameters(default_file_path, run_file_path) model = Model(parameters) setup_forces(parameters, model) # sample the velocities sample_velocities(model.parameters, model.atom_properties) # run the md loop for i in range(1, parameters.n_steps+1): # integrate velocity_verlet(model) model.compute_thermo() berendsen_thermostat(parameters, model.atom_properties, model.thermo_properties)