RSSimTools

OpenMM Wrappers for General and Enhanced MDSimulations

This repo contains several simulation classes wrapped around openMM infrastructure that allow for rapid devlopment and usage of various MD Simulations.

Currently Supported are the following simulations: Minimization, Standard MD (base class); Heating and Equil MD simulations (NVT and NPT respectively), solvent scaled MD, random accelerated MD, and metadynamics MD.

Installation

Dependencies:

RSSimTools requires very few dependencies. Below is a list you can install with conda or pip:

python 3.6 or higher
simtk.openmm
numpy
mdtraj

To install the latest stable version we recommend using pip with the following command (this is the only method guaranteed to provide a stable version).

pip install rs-simtools

Alternatively you can download the source from this repo, navigate to the folder containing setup.py and install locally using

pip install ./

Documentation

Quickstart run

    # Load packages
    import parmed
    from simtk.openmm import unit
    from rs_simtools import MDSimulation, select_atoms
    
    # Note: Requires parameterized parmed in memory named parmed_structure!

    #instantiate sim from parmed alone, minimize (save h5 file) and run
    mdsim = MDSimulation(parmed_structure=parmed_structure)
    mdsim.minimize()
    minimized_parmed = mdsim.run(2 * unit.nanosecond)

    #build sim using a previous trajectory or h5 file
    mdsim = MDSimulation(parmed_structure=parmed_structure, coordinates=trajectory.h5)

    #build sim with positional restraints, run some equilibration and remove them for longer run
    protein_atoms = select_atoms(parmed_structure=parmed_structure, keyword_selection='protein')
    mdsim = MDSimulation(parmed_structure=parmed_structure, atoms_to_restrain=protein_atoms, restraint_weight=4)
    mdsim.run(1*unit.nanosecond)
    mdsim.update_restraint_weight(2)
    mdsim.run(1*unit.nanosecond)
    mdsim.remove_positional_restraints()
    end_parmed = mdsim.run(4 * unit.nanosecond)