Parameterisation, water model

Ferguson D M 1995. Parameterisation and Evaluation of a Flexible Water Model. Journal of Computational Chemistry 16 501-511. 

These classical interaction potentials must be parameterized, e.g. the magnitude of the partial charges on each atom in the molecule must be assigned, and the equilibrium bond length and size of the harmonic force constant must be attached to each bond. In the early biomolecular MM forcefields, these parameters were developed to produce molecular models that could reproduce known experimental properties of the bulk system. For example, several MM water models have been developed. ° One of the earliest successful models, TIP3P, was parameterized such that simulations of boxes of TIP3P molecules reproduced known thermodynamic properties of water, such as liquid density and heats of vaporisation. Such a parameterisation scheme is to be applauded, as it ties the molecular model closely to experiment. Indeed many of the common MM models of amino acids were developed by comparison to experiment, e.g. OPLS. Indeed it is such a good... 

In simulations involving explicit water, it is crucial that a balance exists between water-protein and water-water interactions in order to describe correctly the water-protein interface. This of course depends on the choice of water model to be used with the protein force-field. The developers of most modern force-fields for protein simulations have chosen a specific water model which has then used as the foundation of the force-field parameterisation. In the following we consider the parameter sat ion of the Charmm force-field, although other force-fields have used similar approaches. 

The approach used in the parameterisation procedure means that once a force-field has been developed, it can only be used together with the selected water model. In principle, use of the Charmm22 parameter set with water models other than TIP3P may lead to inconsistencies because the water-protein and protein-protein intermolecular parameterisation may not be well balanced. However, whether this is actually the case has not yet been systematically investigated. 

The meteorological fields are supplied by the limited area model ALADIN-Austria (http //www.cnrm.meteo.fr/aladin/). It is run twice a day at the ZAMG and renders forecasts for 48 h. The meteorological fields have a temporal resolution of 1 h. The data is provided on 45 levels, and model has a horizontal resolution of 9.6 km. Fields of wind, temperatiue, pressure, convective and large scale precipitation, snow cover, solar radiation and specific humidity are extracted directly from the ALADIN dataset. The other fields, cloud optical depth, cloud water- and precipitation water content have to be parameterised (Seinfeld and Pandis 1998) from the ALADIN output. 

Dupont, S., Mestayer, P.G., Guilloteau, E., Berthier, E., and Andrieu, H. (2005) Parameterisation of the Urban Water Budget with the Sub-Meso Soil Model , J. Appl. Meteorol., submitted. 

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