Developing Fast and Accurate Water Models for Atomistic Molecular Dynamics Simulations

Water models are of great importance for different fields of studies such as fluid mechanics, nano materials, and biomolecule simulations. In this dissertation, we focus on the water models applied in atomistic simulations, including those of biomolecules such as proteins and DNA. Despite water's simple structure and countless studies carried out over the decades, the best water models are still far from perfect. Water models are normally divided into two types--explicit model and implicit model. Here my research is mainly focused on explicit models. In explicit water models, fixed charge n-point models are most widely used in atomistic simulations, but have known accuracy drawbacks. Increasing the number of point charges, as well as adding electronic polarizability, are two common strategies for accuracy improvements. Both strategies come at considerable computational cost, which weighs heavily against modest possible accuracy improvements in practical simulations. With a careful comparison between the two strategies, results show that adding polarizability is a more favorable path to take. Optimal point charge approximation (OPCA) method is then applied along with a novel global optimization process, leading to a new polarizable water model OPC3-pol that can reproduce bulk liquid properties of water accurately and run at a speed comparable to 3- and 4-point non-polarizable water models. For practical use, OPC3-pol works with existing non-polarizable AMBER force fields for simulations of globular protein or DNA. In addition, for intrinsically disordered protein simulations, OPC3-pol fixes the over-compactness problem of the previous generation non-polarizable water models.

Name thesis:degree_name

Doctor of Philosophy

Level thesis:degree_level

doctoral

Discipline thesis:degree_discipline

Engineering Mechanics

Department dc:contributor.department

Engineering Science and Mechanics

Grantor dc:publisher

Virginia Tech

Year dc:date.issued

2021

Author dc:creator

• Xiong, Yeyue

Chair dc:contributor.committeechair

• Onufriev, Alexey V.

Committee members dc:contributor.committeemember

• Deshmukh, Sanket A.
• Staples, Anne E.
• De Vita, Raffaella
• Valeyev, Eduard Faritovich

• water model
• molecular dynamics
• global optimization
• polarizable
• Drude

Statement dc:rights

• In Copyright

Licence dc:rights.uri

• http://rightsstatements.org/vocab/InC/1.0/

Dc Identifier Other

vt_gsexam:32429

OAI identifier oai:identifier

oai:vtechworks.lib.vt.edu:10919/105002