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Internet Electronic Journal of Molecular Design - IEJMD, ISSN 1538-6414, CODEN IEJMAT
ABSTRACT - Internet Electron. J. Mol. Des. March 2003, Volume 2, Number 3, 179-194

The Solvent Boundary Potential: A New Approach for Computer Simulation of Large Systems
Valentin Gogonea
Internet Electron. J. Mol. Des. 2003, 2, 179-194

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Abstract:
The paper presents the theoretical framework for the development of a new solvent boundary method for computer simulations and its possible application to the simulation of nitric oxide synthase. Different approaches for the construction of a solvent boundary potential are reviewed and their strengths and weaknesses are discussed. A new solvent boundary potential is proposed which combines the mean field force approximation with the Green's function approach for treating long-range electrostatic interactions, and introduces a novel strategy to treat electrostriction effects due to ions crossing the solvent boundary. Finally, a series of computational tests are devised in order to assess the validity and efficiency of the new solvent boundary potential.

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