Implementation of an Adaptive Umbrella Sampling Method for the Calculation of Multidimensional Potential of Mean Force of Chemical Reactions in Solution

Overview

Journal J Comput Chem

Publisher Wiley

Specialties Biology
Chemistry

Date 2003 Sep 10

PMID 12964196

Citations 12

Authors

Ramkumar Rajamani

Kevin J Naidoo

Jiali Gao

Affiliations

Soon will be listed here.

Abstract

We describe the implementation of an adaptive umbrella sampling method, making use of the weighted histogram analysis method, for computing multidimensional potential of mean force for chemical reaction in solution. The approach is illustrated by investigating the effect of aqueous solution on the free energy surface for the proton transfer reaction of [H(3)N-H-NH(3)](+) using a combined quantum mechanical and molecular mechanical AM1/TIP3P potential.

Citing Articles

Multireference Generalization of the Weighted Thermodynamic Perturbation Method.

Giese T, Zeng J, York D J Phys Chem A. 2022; 126(45):8519-8533.

PMID: 36301936 PMC: 9771595. DOI: 10.1021/acs.jpca.2c06201.

Molecular mechanisms from reaction coordinate graph enabled multidimensional free energies illustrated on water dimer hydrogen bonding.

Bruce-Chwatt T, Naidoo K J Comput Chem. 2022; 43(26):1802-1813.

PMID: 36054751 PMC: 9543413. DOI: 10.1002/jcc.26982.

Exploring the Activation Mechanism of the mGlu5 Transmembrane Domain.

Lans I, Diaz O, Dalton J, Giraldo J Front Mol Biosci. 2020; 7:38.

PMID: 32211419 PMC: 7069277. DOI: 10.3389/fmolb.2020.00038.

Insight into the phosphodiesterase mechanism from combined QM/MM free energy simulations.

Wong K, Gao J FEBS J. 2011; 278(14):2579-95.

PMID: 21595828 PMC: 3128672. DOI: 10.1111/j.1742-4658.2011.08187.x.

Introducing sampling entropy in repository based adaptive umbrella sampling.

Zheng H, Zhang Y J Chem Phys. 2009; 131(21):214105.

PMID: 19968335 PMC: 2802197. DOI: 10.1063/1.3267549.