Berlin 2005 – wissenschaftliches Programm

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AKB: Biologische Physik

AKB 200: Poster Session II

AKB 200.20: Poster

Dienstag, 8. März 2005, 17:00–19:00, Poster TU C

Calculation of solvent entropies from MD simulations — •Friedemann Reinhard and Helmut Grubmüller — MPI für biophysikalische Chemie, Abteilung 070 – Theoretische und computergestützte Biophysik, Am Fassberg 11, 37077 Göttingen

Solvent entropy is the main contribution to the hydrophobic effect. Its computation from molecular dynamics simulations however proves difficult. First, due to the diffusive motion of the solvent molecules, the configuration space is much too large to be sampled sufficiently. Second, the typically very shallow energy landscapes generate phase space densities with quite complex topology.

We address both problems by exploiting the permutation symmetry of the solvent molecules. For every ensemble element generated by the simulation, the water molecules are relabeled such that the permutated configurations fall into a compact volume in phase space. Thereby we greatly enhance sampling without affecting any thermodynamic quantities. Thus the established entropy estimation methods for proteins should become applicable to the relabeled solvent molecules too.

This expectation is confirmed by test calculations on simple model systems. Furthermore, the compactified phase space densities show comparatively simple topology, such that also the second problem is alleviated significantly. What remains to be done is to develop more elaborated density estimates, which is the subject of our current work.