---
title: "Molecular dynamics simulations of biomolecules"
authors: ["Karplus M", "McCammon JA"]
year: 2002
journal: Nature Structural Biology
type: review
tags: [molecular-dynamics, protein-dynamics, simulation]
cited_by: 6200
impact: foundational
nobel_prize: 2013
---

# Molecular dynamics simulations of biomolecules

## Summary

Foundational review of molecular dynamics (MD) for studying protein motion. [[Established]] MD as [[Essential]] tool for understanding protein function through dynamics.

## [[Key Concepts]]

- **Force fields**: [[AMBER Force Field]], [[CHARMM Force Field]]
- **Timescales**: Accessing microsecond dynamics
- **Ensemble sampling**: Conformational space exploration

## Methodology

[[Newtonian Mechanics]] [[Integration]] for [[Protein Conformational Dynamics]]. [[Periodic Boundary Conditions]] for solvent simulation.

## Relevance to My Work

Theoretical basis for [[Protein-Ligand Docking]] refinement. [[AMBER Force Field]] [[Used In]] [[Experiment-2024-11-22]].

## [[Applications]]

- [[Drug Binding Kinetics]]
- [[Allosteric Mechanism]] studies
- [[Protein Folding Pathways]]
