OMMTK
Project description
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)
Project details
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