Parallel Tempering Algorithm for Conformational Studies of Biological Molecules

The effectiveness of a new algorithm, parallel tempering, is studied for numerical simulations of biological molecules. These molecules suffer from a rough energy landscape. The resulting slowing down in numerical simulations is overcome by the new method. This is demonstrated by performing simulations with high statistics for one of the simplest peptides, Met-enkephalin. The numerical effectiveness of the new technique was found to be much better than traditional methods and is comparable to sophisticated methods like generalized ensemble techniques.Comment: Latex, ps-files included; to appear in Chem. Phys. Let

Simulated Annealing with Tsallis Weights - A Numerical Comparison

We discuss the use of Tsallis generalized mechanics in simulated annealing algorithms. For a small peptide it is shown that older implementations are not more effective than regular simulated annealing in finding ground state configurations. We propose a new implementation which leads to an improvement over regular simulated annealing.Comment: Late

On non-round points of the boundary of the numerical range and an application to non-selfadjoint Schr\"odinger operators

We show that non-round boundary points of the numerical range of an unbounded operator (i.e. points where the boundary has infinite curvature) are contained in the spectrum of the operator. Moreover, we show that non-round boundary points, which are not corner points, lie in the essential spectrum. This generalizes results of H\"ubner, Farid, Spitkovsky and Salinas and Velasco for the case of bounded operators. We apply our results to non-selfadjoint Schr\"odinger operators, showing that in this case the boundary of the numerical range can be non-round only at points where it hits the essential spectrum.Comment: Shortened version. To appear in Journal of Spectral Theor

Stochastic dynamics simulations in a new generalized ensemble

We develop a formulation for molecular dynamics, Langevin, and hybrid Monte Carlo algorithms in the recently proposed generalized ensemble that is based on a physically motivated realisation of Tsallis weights. The effectiveness of the methods are tested with an energy function for a protein system. Simulations in this generalized ensemble by the three methods are performed for a penta peptide, Met-enkephalin. For each algorithm, it is shown that from only one simulation run one can not only find the global-minimum-energy conformation but also obtain probability distributions in canonical ensemble at any temperature, which allows the calculation of any thermodynamic quantity as a function of temperature.Comment: to appear in Chem. Phy. Let

Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape

We propose two efficient algorithms for configurational sampling of systems with rough energy landscape. The first one is a new method for the determination of the multicanonical weight factor. In this method a short replica-exchange simulation is performed and the multicanonical weight factor is obtained by the multiple-histogram reweighting techniques. The second one is a further extension of the first in which a replica-exchange multicanonical simulation is performed with a small number of replicas. These new algorithms are particularly useful for studying the protein folding problem.Comment: 9 pages, (ReVTeX), 7 figures. Chem. Phys. Lett. (2000), in pres