Berlin 2015 – wissenschaftliches Programm

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DY: Fachverband Dynamik und Statistische Physik

DY 56: Poster - Statistical Physics

DY 56.17: Poster

Donnerstag, 19. März 2015, 16:00–18:00, Poster A

Markov State Model with reweighting: application to small molecules with perturbed potential — Luca Donati and •Bettina Keller — Freie Universität Berlin, Berlin, Germany

We have studied the effect of small perturbations in the potential energy surface of molecular systems by performing numerical simulations and constructing Markov State Model of the trajectories. The Markov State Models are a valid tool to analyze the large amounts of data generated by Molecular Dynamics simulations and to extract information on the timescales. In general, it is necessary to perform a new simulation after having changed the potential to construct the Markov State Model of the perturbed molecule. However, if we consider small perturbations of the system, we can use reweighting methods [1] to construct a Markov State Model that does not need a new simulation, but that uses the trajectory of the initial not-perturbed molecule. Our method is based on the Girsanov theorem [2], that has been already tested successfully for diffusive processes (e.g. a double well potential perturbed by an external force). We applied it on small molecules subjected to alchemical transformations. We studied the effect of varying the charges and the van der Waals radii on the conformational dynamics. The approach is relevant to force-field optimization, but it could eventually also be used to study mutations in proteins.

[1] Jan-Hendrik Prinz et.al., The Journal of Chemical Physics, 134, 2011

[2] Schütte Christof et.al., Molecular Physics, 00, 2014