Overview

StreaMD is a toolkit to run high-throughput molecular dynamics simulations end-to-end: preparation, equilibration, production, continuation, and analysis.

Description

• Fully automated pipeline for molecular dynamics

• Supports proteins in water, protein-ligand, protein-cofactor, and combined protein-ligand-cofactor systems

• Gaussian and MCPB.py integration for boron-containing compounds and metalloproteins

• Distributed computing via Dask with CPU/GPU balancing

• Multiple replicas in a single command

• Restartable: extend or continue interrupted runs safely

• Built-in analysis (RMSD, RMSF, radius of gyration) plus MM/PB(GB)SA and ProLIF utilities

• Custom .mdp files

• GPU support

Next Steps

• Set up the environment: see Installation

• Prepare inputs: see Input Preparation

• Run simulations: see Running Molecular Dynamics

• Explore outputs and analysis: see Outputs and Files, MM-PBSA/MM-GBSA Calculations, ProLIF (Protein-Ligand Interaction Fingerprints) Analysis, and Trajectory Convergence Analysis