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September 10, 2025The Journal of Physical Chemistry B

Simulating Biomolecules with the Variable Protonation State: A Tutorial for Constant-pH Molecular Dynamics in NAMD

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Authors

SMSarah MoeBRBrian K. RadakCCChristophe Chipot

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Overview

This tutorial demonstrates constant-pH molecular dynamics simulations of biomolecules, highlighting protonation state variations and their analysis.

Key Points

  • Constant-pH simulations actively explore multiple protonation states, enhancing modeling accuracy.
  • The method produces titration curves that can be directly compared to experimental data.
  • Molecular dynamics typically assumes fixed protonation states, which this technique aims to improve.
  • Using NAMD for simulations facilitates the study of dynamic protonation changes in biomolecules.

Cite This Study

Moe et al. (2025) studied this question.

synapsesocial.com/papers/68c1afd354b1d3bfb60e803fhttps://doi.org/10.1021/acs.jpcb.5c03069
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