TOPO: TOPOlogy-based coarse-grained model for folded prOteins

A coarse-grained simulation engine for globular (folded) proteins using OpenMM. TOPO builds topology/structure-based models with bonds, angles, periodic torsions, electrostatics, and optional contact-based non-bonded interactions.

Requirements

• OpenMM ≥ 7.7
• Parmed
• See requirements.txt for full list.

Install

# Clone or download the repo, then add to Python path (project root = parent of topo/)
export PYTHONPATH=$PYTHONPATH:/path/to/topo

Install dependencies (e.g. conda): conda install -c conda-forge openmm parmed (and others from requirements.txt). mamba is recommemded for performance and speed to install

Usage

From an example directory:

cd examples/standard_example
python run_simulation.py -f md.ini

Or run the top-level script:

python topo/topo-simulation.py -f md.ini

Use a control file (e.g. md.ini) with options such as: md_steps, dt, pdb_file, model (use topo), box_dimension, device, etc. See examples/standard_example/md.ini for a template.

Contact

Report issues to Quyen Vu (vuqv.phys@gmail.com).