Titlebook: Computational Molecular Dynamics: Challenges, Methods, Ideas; Proceeding of the 2n Peter Deuflhard,Jan Hermans,Robert D. Skeel Conference p

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https://doi.org/10.1007/978-3-030-64616-5ble, semi-implicit methods. Here semi-implicit means that only the highly oscillatory part is integrated by an implicit method such as the midpoint method or an energy-conserving variant of it. The hope is that such methods will allow one to use a step-size . which is much larger than the period . of the fast oscillations.

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Computational Molecular Dynamics: Challenges, Methods, IdeasProceeding of the 2n

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Computation of Essential Molecular Dynamics by Subdivision Techniquesctory simulation on the other hand: in our setup long term trajectories are replaced by short term sub-trajectories, Monte-Carlo techniques are connected via the underlying Frobenius-Perron structure. Numerical experiments with the suggested algorithm are included to illustrate certain distinguishin

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Exploration of Peptide Free Energy Surfacesminima are further refined by the novel procedure of free energy optimization by steepest descent down the gradient, leading to structures in excellent agreement with experimental data. The stability of the minima with respect to deformations is studied by analysis of second derivatives of the free

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Prediction of pKas of Titratable Residues in Proteins Using a Poisson-Boltzmann Model of the Solute-ow-energy ionization states out of all possible states, to obtain a correct estimation of thermodynamic properties of the system..As examples of applications, we present the overall accuracy of predicted ionization constants for about 50 groups in 4 proteins, changes in the average charge of bovine

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