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Three-site and five-site fixed-charge water models compatible with AMOEBA force field
Cong Pan1, Chengwen Liu2, Junhui Peng1
1Department of Chemistry, The Hong Kong University of Science and Technology, Hong Kong.
Journal of Computational Chemistry
|January 25, 2020
Summary
We developed two new water models, AW3C and AW5C, compatible with the AMOEBA force field. These models significantly accelerate biomolecular simulations while maintaining accuracy, offering a more efficient approach for computational studies.
Area of Science:
- Computational Chemistry
- Biomolecular Modeling
- Force Field Development
Background:
- Biomolecular simulations using the AMOEBA force field are computationally intensive, largely due to the explicit treatment of water molecules and their mutual induction effects.
- Existing water models can limit the efficiency of large-scale simulations.
Purpose of the Study:
- To develop computationally efficient, nonpolarizable water models compatible with the AMOEBA force field.
- To improve the speed of biomolecular simulations without sacrificing accuracy.
Main Methods:
- Developed two new water models: 3-site AW3C and 5-site AW5C, with flexible bonds and fixed charges.
- Parameterized AW3C and AW5C using six experimental thermodynamic properties across a wide temperature range (261.15–353.15 K).
- Validated models by comparing radial distribution functions, self-diffusion constants, and hydration free energies against experimental data and the AMOEBA03 water model.
Main Results:
- AW3C and AW5C models successfully reproduce key experimental liquid properties and simulation results.
- These new models accelerate bulk water and biomolecular simulations by over 5 times compared to the standard AMOEBA water model.
- Simulations of a DNA duplex using AW3C/AW5C showed a threefold acceleration while preserving structural integrity.
Conclusions:
- AW3C and AW5C offer a significant computational speed-up for AMOEBA-based biomolecular simulations.
- These models provide a promising alternative for simulating complex biological systems efficiently.
- The developed water models maintain the accuracy of structural properties crucial for biological insights.
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