An algorithm and software to refine parameters of empirical energy functions according to condensed phase experimental measurements are discussed. The algorithm is based on sensitivity analysis and local minimization of the differences between experiment and simulation as a function of potential parameters. It is illustrated for a toy problem of alanine dipeptide and is applied to folding of the peptide WAAAH. The helix fraction is highly sensitive to the potential parameters while the slope of the melting curve is not. The sensitivity variations make it difficult to satisfy both observations simultaneously. We conjecture that there is no set of parameters that reproduces experimental melting curves of short peptides that are modeled with the usual functional form of a force field.
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| http://dx.doi.org/10.1021/ct400313n | DOI Listing |
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