30,539 research outputs found

    Evaluating force field accuracy with long-time simulations of a tryptophan zipper peptide

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    We have combined a custom implementation of the fast multiple-time-stepping LN integrator with parallel tempering to explore folding properties of small peptides in implicit solvent on the time scale of microseconds. We applied this algorithm to the synthetic {\beta}-hairpin trpzip2 and one of its sequence variants W2W9. Each simulation consisted of over 12 {\mu}s of aggregated virtual time. Several measures of folding behavior showed convergence, allowing comparison with experimental equilibrium properties. Our simulations suggest that the electrostatic interaction of tryptophan sidechains is responsible for much of the stability of the native fold. We conclude that the ff99 force field combined with ff96 {\phi} and {\psi} dihedral energies and implicit solvent can reproduce plausible folding behavior in both trpzip2 and W2W9.Comment: 10 pages, 11 figures, submitted to the Journal of Chemical Physics on June 28, 201

    Fluctuation-induced interactions between dielectrics in general geometries

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    We study thermal Casimir and quantum non-retarded Lifshitz interactions between dielectrics in general geometries. We map the calculation of the classical partition function onto a determinant which we discretize and evaluate with the help of Cholesky factorization. The quantum partition function is treated by path integral quantization of a set of interacting dipoles and reduces to a product of determinants. We compare the approximations of pairwise additivity and proximity force with our numerical methods. We propose a ``factorization approximation'' which gives rather good numerical results in the geometries that we study
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