1. 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. Main Objectives

2. Intuitive graphical user interface for easy configuration of molecular modeling parameters. Flexible scripting language to drive the underlying C library. Wrapped C structures and functions provide interface to high level scripting language. Molecular modeling C library. Scripting Language GUI Interface C Library API Hierarchy

3. Molecular model: - stretching: Harmonic, Morse - bending: Harmonic,  -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 C Library Functionality

4. C structures atom_properties ff_properties. Python objects atom_properties ff_properties. SWIG C functions compute_tot_forces() compute_thermo(). Python functions compute_tot_forces() compute_thermo(). SWIG Library to Scripting Language Mapping

5. Forces Class Diagram # 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() Python script to add force contributions to model

6. 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) MD Script