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    Optimization of force fields for molecular dynamics

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    DIPIERRO-DISSERTATION-2014.pdf (11.59Mb)
    Date
    2014-12
    Author
    Di Pierro, Michele
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    Abstract
    A technology for optimization of potential parameters from condensed phase simulations (POP) is discussed and illustrated. It is based on direct calculations of the derivatives of macroscopic observables with respect to the potential parameters. The derivatives are used in a local minimization scheme, comparing simulated and experimental data. In particular, we show that the Newton Trust-Region protocol allows for accurate and robust optimization. POP 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. We then apply the newly developed technology to study the liquid mixture of tert-butanol and water. We are able to obtain, after 4 iterations, the correct phase behavior and accurately predict the value of the Kirkwood Buff (KB) integrals. We further illustrate that a potential that is determined solely by KB information, or the pair correlation function, is not necessarily unique.
    Department
    Computational Science, Engineering, and Mathematics
    Description
    text
    Subject
    Molecular dynamics
    Optimization
    Force field
    Peptide
    Tert-butanol
    Butyl alcohol
    Tert-butyl
    Parameters refinement
    Molecular mechanics
    Melting curve
    Newton Method
    Simulation
    Biophysics
    Kirkwood-Buff
    Trust region
    URI
    http://hdl.handle.net/2152/28355
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