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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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