Regensburg 2016 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 20: Posters - Molecular Dynamics

BP 20.3: Poster

Montag, 7. März 2016, 17:30–19:30, Poster C

Quantitative assessment of sampling quality of molecular dynamics simulations of biomolecular systems — •Mike Nemec and Daniel Hoffmann — Bioinformatics - Center for Medical Biotechnology, University of Essen, Germany

Typical biomolecular systems have huge, rugged energy landscapes. Although Molecular Dynamics (MD) simulations only sample tiny fractions of these landscapes, these samples are often used for inferring properties of the biomolecular systems, such as thermodynamic averages or conformational states. It is therefore a critical question, how well MD simulations actually sample these systems. Here we show how the quality of the sampling can be assessed by a combination of two measures, the mixture of configurations between MD trajectories and the effective sample size. We report numerical results from extensive MD simulations of two polypeptides in aqueous solution, Met-Enkephalin (5 residues) and HIV-1 gp120 V3 (35 residues), with various sampling protocols, namely conventional MD and two enhanced sampling algorithms aMD and scaledMD.