Minimal Coacervates: Molecular Dynamics Simulations

This repository contains example scripts for running and analyzing the atomistic and coarse-grained molecular dynamics simulations from our paper: "Differential stability and dynamics of DNA-based and RNA-based coacervates affect non-enzymatic RNA chemistry", Karina K Nakashima, Fatma Zohra Mihoubi, Jagandeep S Saraya, Kieran O Russell, Fidan Rahmatova, James D Robinson, Maria Julia Maristany, Jan Huertas, Roger Rubio Sanchez, Rosana Collepardo Guevara, Derek K O'Flaherty, Claudia Bonfio, Nature Communications.

Please use freely and cite our publication, raise any questions as an issue on this repository or email to Kieran Russell, kor20@cam.ac.uk.

Repository Structure

paper_scripts/
├── simulation_scripts/
│   ├── atomistic/
│   └── coarse_grained/
├── analysis_scripts/
│   ├── analyse_cg_contacts.py
│   ├── analyse_cg_density.py
│   └── analyse_contact_types.py
├── requirements.txt
└── README.md

Usage

Simulation

The simulation_scripts directory contains scripts for running both atomistic and coarse-grained simulations. Refer to the README.md within that directory for detailed instructions.

Analysis

The analysis_scripts directory contains scripts for analyzing simulation trajectories. Refer to the README.md within that directory for detailed instructions.

Dependencies

• OpenMM
• MDTraj
• NumPy
• Pandas
• CuPy (for GPU-accelerated analysis)
• Matplotlib
• Python 3

See requirements.txt for a full list of dependencies.