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Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

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Best Practices in Constant pH MD Simulations: Accuracy and Sampling.

Pavel Buslaev¹, Noora Aho¹, Anton Jansen²

¹Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014 Jyväskylä, Finland.

Journal of Chemical Theory and Computation

|September 15, 2022

Summary

This summary is machine-generated.

This study provides guidelines for accurate long time scale constant pH molecular dynamics (MD) simulations. Small force field modifications and higher-order fits improve convergence and pKa predictions.

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Area of Science:

Computational Chemistry
Biomolecular Simulation
Physical Chemistry

Background:

Accurate molecular dynamics (MD) simulations require incorporating pH effects.
The lambda-dynamics approach offers a computationally efficient method for pH-dependent MD.
Long time scale simulations necessitate critical evaluation of force fields and parameterization.

Purpose of the Study:

To provide guidelines for setting up and performing long time scale constant pH MD simulations.
To address accuracy and sampling issues in microsecond time scale simulations.
To enable widespread application of constant pH MD beyond pKa prediction.

Main Methods:

Utilized the lambda-dynamics approach for constant pH MD simulations.
Proposed minor modifications to the CHARMM36m force field to reduce torsional barriers.
Employed higher-order polynomial fits for correction potentials.

Main Results:

Modified force field achieved converged protonation and torsional distributions.
Consistent pKa estimates were obtained with the proposed modifications.
Higher-order fits for correction potentials proved essential for accuracy.

Conclusions:

Small force field adjustments and accurate correction potentials are crucial for reliable constant pH MD.
The developed methods enhance the accuracy and sampling efficiency of MD simulations.
This work facilitates broader use of constant pH MD in various applications.