Potential truncation effects in molecular simulations.
Technische Universität, Darmstadt
[Ph.D. Thesis], (2006)
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|Item Type:||Ph.D. Thesis|
|Title:||Potential truncation effects in molecular simulations|
Hdration has an important influence on biomolecular processes in aqueous solution like ligand binding or structure and function of proteins. The computer based molecular simulation technique provides a tool to calculate macroscopic structural and thermodynamic properties of liquids and solute/solvent systems, for example radial distribution functions or free energies of solvation. A classical molecular dynamic simulation at atomic level is a computational demanding task. The efficiency is considerably increased by using empirical interaction potentials with spherical truncation conditions and small simulation boxes. The efficient simulation conditions are known to evoke systematic errors in calculated observables. The limited number of molecules in the simulation box generates a finite size effect whereas the approximation of interaction potentials causes a truncation effect. Finite size effects can only be avoided by increasing the system size, but truncation effects can be reduced or corrected with appropriate simulation algorithms. The key idea of this work is to improve the efficiency of molecular dynamic simulation of liquids by applying small spherical truncation distances and minimize or correct the truncation errors. The first employed strategy is restricted to polar liquids like water. Considering the dielectric properties of the medium an effective Coulomb potential is constructed and parameterized for some water models. Several observables are calculated with small truncation distances and shown to be very close to the corresponding Ewald summation reference values. The second technique is based on the combination of molecular simulation and one dimensional RISM integral equation theory. Comparing the radial distribution functions of water indeqendently generated by simulation and by RISM theory it is noticed that both exhibit exactly the same truncation effect. Thus with RISM theory the truncation errors of simulation results can be corrected. Using thermodynamic integration the absolute hydration free energy of argon in water and the electrostatic contribution to the excess chemical potential of water are calculated with various truncation conditions. The RISM correction is capable to reliably predict the truncation effects. The new RISM correction method is successfully applied to the efficient simulation of radial distribution functions, excess potential energy and finally the free energy of hydration.
|Place of Publication:||Darmstadt|
|Classification DDC:||500 Naturwissenschaften und Mathematik > 540 Chemie|
|Divisions:||07 Fachbereich Chemie|
|Date Deposited:||17 Oct 2008 09:22|
|Last Modified:||07 Dec 2012 11:51|
|Referees:||Lindner, Prof.Dr. Hans Jörg|
|Advisors:||Brickmann, Prof.Dr. Jürgen|
|Refereed:||24 October 2005|