IMAGE CHARGE SOLVATION MODEL (ICSM) FOR SIMULATING BIOMOLECULES AND KCSA ION-CHANNELS

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Baker, K. (2014). IMAGE CHARGE SOLVATION MODEL (ICSM) FOR SIMULATING BIOMOLECULES AND KCSA ION-CHANNELS. Unc Charlotte Electronic Theses And Dissertations.
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Abstract

We present an order N method for calculating electrostatic interactions that has been integrated into the molecular dynamics portion of the TINKER Molecular Modeling package. This method, termed the Image-Charge Solvation Model (ICSM), and introduced previously by Dr. Lin et al. (1) in 2009, is a hybrid electrostatic approach that combines the strengths of both explicit and implicit representations of the solvent. In this model, a multiple-image method is used to calculate reaction fields due to the implicit solvent while the Fast Multipole Method (FMM) is used to calculate the Coulomb interactions for all charges, including the charges in the explicit solvent part.The integrated package is validated through simulations of liquid water. The results are compared with those obtained by the Particle Mesh Ewald (PME) method that is built in the TINKER package. Timing performance of TINKER with the integrated ICSM is benchmarked on bulk water as a function of the size of the system. In particular, timing analysis results show that the ICSM outperforms the PME for sufficiently large systems with the break-even point at around 30,000 particles in the simulated system. To demonstrate the capability of the package on large macromolecules, the model is used to simulate the potassium channel KcsA.

Details
Author

Baker, Katherine

Title

IMAGE CHARGE SOLVATION MODEL (ICSM) FOR SIMULATING BIOMOLECULES AND KCSA ION-CHANNELS

Physical Description

1 online resource (78 pages) : PDF

Date

2014

Degree Granting Institution

University of North Carolina at Charlotte

Abstract

We present an order N method for calculating electrostatic interactions that has been integrated into the molecular dynamics portion of the TINKER Molecular Modeling package. This method, termed the Image-Charge Solvation Model (ICSM), and introduced previously by Dr. Lin et al. (1) in 2009, is a hybrid electrostatic approach that combines the strengths of both explicit and implicit representations of the solvent. In this model, a multiple-image method is used to calculate reaction fields due to the implicit solvent while the Fast Multipole Method (FMM) is used to calculate the Coulomb interactions for all charges, including the charges in the explicit solvent part.The integrated package is validated through simulations of liquid water. The results are compared with those obtained by the Particle Mesh Ewald (PME) method that is built in the TINKER package. Timing performance of TINKER with the integrated ICSM is benchmarked on bulk water as a function of the size of the system. In particular, timing analysis results show that the ICSM outperforms the PME for sufficiently large systems with the break-even point at around 30,000 particles in the simulated system. To demonstrate the capability of the package on large macromolecules, the model is used to simulate the potassium channel KcsA.

Genre

doctoral dissertations

Subjects--Topics

Mathematics

Degree

Ph.D.

Keywords

Molecular Dynamics
Potassium Ion Channel

Subject Area

Mathematics

Advisor(s)

Cai, Wei

Committee Members

Deng, Shaozhong
Chen, Duan
Wu, Xintao

Degree Note

Thesis (Ph.D.)--University of North Carolina at Charlotte, 2014.

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Rights Holder Information

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Identifier

Baker_uncc_0694D_10628

Permalink

http://hdl.handle.net/20.500.13093/etd:89