Sensitivity Results on the Choice of Force Fields

DEPENDENCE OF SENSITIVITY RESULTS ON THE CHOICE OF FORCE FIELDS 

Depending on the force field used in a molecular dynamics or a Monte Carlo simulation, sensitivity coefficients with apparently similar forms may have very different values. For example, the electrostatic energy of a biomolecule in solution may be modeled by using Coulomb s law with effective atomic partial charges that implicitly approximate the effects of electronic polarization of the atoms of the biomolecule by their surroundings. On the other hand, explicit polarization terms can also be used in a force field to calculate the electrostatic energy of a system. 

If one calculates the sensitivity coefficients of different properties of an aqueous system with respect to the atomic partial charges of the water models, the sensitivity coefficients obtained from an effective charge model can be different from those of a polarizable model. This difference was found in calculations of the charge sensitivities of different properties of liquid water with two effective charge models (the SPC and the TIP3P models ) and a polarizable water model (Table 1), although the differences were more pronounced for sensitivity coefficients of some types than for others. Therefore, in using sensitivity coefficients to help identify the determinants of bio(molecular) proper- 

Therefore, just as in genetic studies, in which different point mutations may reflect different determining factors of the properties of a protein, the perturbation of apparently similar parameters of potential models of different types may reflect different determining factors of the properties of a biomolecular system. A user of sensitivity analysis needs to keep this in mind to make proper inferences from sensitivity data. 

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