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Coarse-graned Intermolecular Potentials Derived From the Effective Fragment Potential: Application to Water, Benzene and Carbon Tetrachloride
Multi-scale Quantum Models for Biocatalysis (2009)
  • Gaurav Pranami
  • Monica H. Lamm, Iowa State University
  • Mark S. Gordon
  • Lyudmila V. Slipchenko, Iowa State University
Abstract
A force matching technique based on previous work by Voth and co-workers is devel- oped and employed to coarse grain intermolecular potentials for three common solvents: carbon tetrachloride, benzene, and water. The accuracy of the force-matching approach is tested by comparing radial distribution functions (RDF) obtained from simulations using the atomistic and coarse-grained potentials. Atomistic molecular dynamics simulations were performed using the effective fragment potential method (EFP). The RDFs obtained from molecular dynamics simulations of EFPs for carbon tetrachloride, benzene and water are in a good agreement with the corresponding experimental data. The coarse-grained potentials reproduce the EFP molecular dynamics center-of-mass RDFs with reasonable accuracy. The biggest discrepancies are observed for benzene, while the coarse-graining of water and spherically symmetric carbon tetrachloride is of better quality.
Keywords
  • Coarse-graining,
  • Force-matching,
  • Effective fragment potential method,
  • Molecular dynamics,
  • Radial distribution functions,
  • Multiscale modeling
Publication Date
Spring April 15, 2009
DOI
10.1007/978-1-4020-9956-4
Publisher Statement
Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications explores various molecular modelling techniques and their applications in providing an understanding of the detailed mechanisms at play during biocatalysis in enzyme and ribozyme systems. These areas are reviewed by an international team of experts in theoretical, computational chemistry, and biophysics.

This book has three sections that group together different aspects of multi-scale quantum simulations. The first section consists of four chapters that describe strategies for multi-scale quantum models and present an overview of the current state-of-the-art molecular modelling methodologies most relevant to handling these complex systems with quantum mechanics and molecular simulation. With five chapters, the second section mainly focuses on the current efforts to improve the accuracy of quantum calculations using simplified empirical model forms. The last section consists of five chapters focused on the applications of important biological systems using multi-scale quantum models. This book presents detailed reviews concerning the development of various techniques, including ab initio molecular dynamics, density functional theory, combined QM/MM methods, solvation models, force field methods, and free-energy estimation techniques, as well as successful applications of multi-scale methods in the biocatalysis systems including several protein enzymes and ribozymes.
Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications is an excellent source of information for research professionals involved in computational chemistry and physics, material science, nanotechnology, rational drug design and molecular biology. It is also likely to be of interest to graduate and undergraduate students exposed to these research areas.
Citation Information
Gaurav Pranami, Monica H. Lamm, Mark S. Gordon and Lyudmila V. Slipchenko. "Coarse-graned Intermolecular Potentials Derived From the Effective Fragment Potential: Application to Water, Benzene and Carbon Tetrachloride" Multi-scale Quantum Models for Biocatalysis (2009)
Available at: http://works.bepress.com/monica_lamm/27/