In complex systems with many degrees of freedom such as peptides and proteins, there
exists a huge number of local‐minimum‐energy states. Conventional simulations in the …

Over the past three decades, a number of powerful simulation algorithms have been
introduced to the protein folding problem. For many years, the emphasis has been placed on …

GROMACS is one of the most widely used open-source and free software codes in
chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of …

We have developed a formulation for molecular dynamics algorithm for the replica-
exchange method. The effectiveness of the method for the protein-folding problem is tested …

This book provides a self-contained and up-to-date treatment of the Monte Carlo method
and develops a common framework under which various Monte Carlo techniques can be" …

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 …

We have developed a new simulation algorithm for free-energy calculations. The method is
a multidimensional extension of the replica-exchange method. While pairs of replicas with …

We present the latest version of the Groningen Molecular Simulation program package,
GROMOS05. It has been developed for the dynamical modelling of (bio) molecules using …

Markov Chain Monte Carlo (MCMC) methods are now an indispensable tool in scientific
computing. This book discusses recent developments of MCMC methods with an emphasis …

In complex systems with many degrees of freedom such as spin glass and biomolecular
systems, conventional simulations in canonical ensemble suffer from the quasi-ergodicity …