Accounting for polarization in molecular simulation



Publication Details

Yu, H. & van Gunsteren, W. (2005). Accounting for polarization in molecular simulation. Computer Physics Communications, 172 (2), 69-85.


Polarization plays an important role in the energetics of molecular systems, not the least in biomolecular systems. Most computer simulation studies of such systems do not treat electronic polarizability explicitly, but only implicitly using effective charges, dielectric permittivities or continuum electrostatics methods. Yet, the introduction of explicit polarizability into biomolecular models and force fields is unavoidable when more accurate simulation results are to be obtained. Various ways to account for polarizability in (bio)molecular simulation are reviewed with an eye to striking a balance between accuracy on the one hand and simplicity and computational efficiency on the other. The various choices to be made are listed and discussed. The most promising approach, the so-called Charge-On-Spring type of models, is treated in more detail and applied to liquid water as an example. Its implementation in the GROMOS biomolecular simulation software is sketched.

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