On using oscillating time-dependent restraints in MD simulation

The use of time-dependent restraints in molecular simulation in order to generate a conformational ensemble for molecules that is in accordance with measured ensemble averages for particular observable quantities is investigated. Using a model system consisting of liquid butane and the cyclic peptide antamanide the reproduction of particular average (3)J-coupling constant values in a molecular dynamics simulation is analysed. It is shown that the multiple-valuedness and the sizeable gradients of the Karplus curve relating (3)J-coupling constants measured in NMR experiments to the corresponding torsional-angle values cause severe problems when trying to restrain a (3)J-coupling constant to a value close to the extrema of the Karplus curve. The introduction of a factor oscillating with time into the restraining penalty function alleviates this problem and enhances the restrained conformational sampling

On the transferability of the SPCAL water model to biomolecular simulation

We investigated the performance of the recently developed SPC/L model for liquid water, as a pure liquid, in binary mixtures with DMSO, and as a solvent model in a peptide folding simulation. Additionally, in order to test the compatibility with the GROMOS biomolecular force field, free energies of hydration of a set of representative compounds were computed. The results are compared to those for the well established SPC water model, which is generally used as a solvent model in conjunction with the GROMOS force field already for more than two decades. It turns out that as a pure liquid and in binary mixtures with DMSO the SPC/L model outperforms SPC, whereas as solvent in combination with the GROMOS force field both models perform equally well

Molecular dynamics simulation of biomolecular systems

The group for computer-aided chemistry at the ETH Zurich focuses its research on the development of methodology to simulate the behavior of biomolecular systems and the use of simulation techniques to analyze and understand biomolecular processes at the atomic level. Here, the current research directions are briefly reviewed and illustrated with a few examples

Kalvinismus Und Kapitalismus

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