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Thermostats As we have presented it so far, molecular dynamics is performed in the microcanonical ensemble of constant NVE variables (and technically also: total momentum P). We found that we could estimate the temperature using thermodynamic averages. It is often desirable, however, to specify the temperature a priori and perform a simulation in the canonical ensemble. There are several approa...

A Reduced Basis Method for Molecular Dynamics Simulation

On the basis of empirical evidence from molecular dynamics simulations, molecular conformational space can be described by means of a partition of central conical regions (cells) characterized by the dominance relations between cartesian coordinates. This work presents a geometric and combinatorial description of the cell arrangement which is polar to a 3x(N-1)-dimensional polytope. Conformatio...

für Naturforschung in cooperation with the Max Planck Society for the Advancement of Science under a Creative Commons Attribution 4.0 International License. Dieses Werk wurde im Jahr 2013 vom Verlag Zeitschrift für Naturforschung in Zusammenarbeit mit der Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. digitalisiert und unter folgender Lizenz veröffentlicht: Creative Commons Namen...