Re: [GaMD-discuss] Calculation of association and dissociation rate constant

[Miao, Y. <Yin...@me...>]

Dear Jessi,

For kinetic reweighting of LiGaMD simulations, we hope to put together a tutorial in the near future. Meanwhile, you may refer to our GaMD analysis webpage: https://www.med.unc.edu/pharm/miaolab/resources/gamd/analysis/
Kinetic reweighting of GaMD simulations with Kramers’ Rate Theory

Reweighting of biomolecular kinetics from GaMD simulations can be obtained by applying Kramers rate theory. The curvatures and energy barriers of the reweighted and modified free energy profiles, as well as the apparent diffusion coefficients, are calculated and used in Kramers’ rate equation to determine accelerations of biomolecular kinetics and recover the original biomolecular kinetic rate constants from the GaMD simulations. In addition to “PyReweighting” that facilitates calculations of free energy profiles, a Smoluchowski equation solver coded in C++ (“smol_solver” shared by Prof. Donald Hamelberg) can be used to calculate kinetic rates across PMF free energy barriers as needed to estimate the apparent diffusion coefficients.

Download the source code and test examples, along with compiling and usage instructions included in a README file<https://github.com/MiaoLab20/smol_solver>

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And “APPENDIX C: REWEIGHTING OF BIOMOLECULAR KINETICS WITH KRAMERS’ RATE THEORY” in the LiGaMD paper: https://pubs.acs.org/doi/10.1021/acs.jctc.0c00395?ref=pdf

Hope these are helpful! Please let me know if you have any further questions.

Best,
Yinglong

Yinglong Miao, Ph.D.
Associate Professor
Department of Pharmacology
Computational Medicine Program
Lineberger Comprehensive Cancer Center
University of North Carolina - Chapel Hill
Tel: 1-919-962-5696
http://miaolab.org

Editor-in-Chief
npj Drug Discovery
https://www.nature.com/npjdrugdiscov

On Feb 5, 2026, at 9:18 AM, Chan, Jessi <jes...@ku...> wrote:

Dear Professor Miao,

My name is Jessi, a graduate student from Department of Pharmaceutical Chemistry, University of Kansas. I am working on a protein-ligand complex using LiGAMD3, particularly interested on getting the binding rate constant. I noticed that in the tutorial there is no section for the calculation . Would you mind sharing more details or the scripts for the calculation?

Looking forward to hearing from you. Thank you so much.

Best regards,
Jessi
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