Usage Guide

Installation

Install the dependencies:

pip install numpy MDAnalysis scipy

Running a Simulation

A basic simulation involves defining a system, a forcefield, and an integrator.

from synth_dynamics import System, ANMForceField, LangevinIntegrator, Simulation

# 1. Load the system (C-alpha atoms)
system = System("protein.pdb")

# 2. Define the Anisotropic Network Model forcefield
ff = ANMForceField(system.equilibrium_coords, cutoff=15.0, spring_constant=1.0)

# 3. Choose an integrator
integrator = LangevinIntegrator(dt=0.1, temperature=300.0, friction=1.0)

# 4. Run the simulation
sim = Simulation(system, ff, integrator)
sim.run(n_steps=1000, output_path="trajectory.dcd", stride=10)

Key Components

  • System: Handles PDB loading and coordinate management.

  • ANMForceField: Computes harmonic forces based on the Elastic Network Model.

  • LangevinIntegrator: Propagates coordinates using the overdamped Langevin equation.

  • Simulation: Orchestrates the run and writes output trajectories.