Publication: The implementation of polarizable and flexible models in molecular dynamics simulations

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Title	The implementation of polarizable and flexible models in molecular dynamics simulations
Authors/Editors*	S. Wang, N. M. Cann
Where published*	HPCS'09 conference proceedings
How published*	Book
Year*	2010
Volume
Number
Pages	34
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Abstract	We discuss a new methodology for implementing polarizable and flexible molecular models - the fluctuating charge and intramolecular potential (fCINTRA) method - in Molecular Dynamics (MD) simulations. An example has been provided for ethanol. In these models, all potential parameters depend on the local electrostatic field generated by the other molecules in the system. A methodology for extracting field-dependent intramolecular potentials from ab initio calculations is discussed, and the parameters controlling the energetics of intramolecular motion are directly coupled to the field experienced by the atoms in a molecule. Variability in the atomic charges is introduced via the fluctuating charge model of Rick et al. [S. Rick, et al., J. Chem. Phys. 1994, 101, (7), 6141-6156.]. Atomic charge fluctuations are much faster than atomic motion and, for practical reasons, a multiple time steps algorithm is required. In the implementation of MD simulations for this model, the Message Passing Interface (MPI) has been used. The simulation algorithm is complex for the fCINTRA model. However, with the help of load sharing, minimization of interprocessor communications, and code optimization, the overall simulation time is acceptable.