16 citations · 20 across the 3 of their papers we have counts for
6 papers · 1 filter
Thermodynamics of two lattice ice models in three dimensions
Chizuru Muguruma, Yuko Okamoto, Bernd A. Berg
In a recent paper we introduced two Potts-like models in three dimensions, which share the following properties: (A) One of the ice rules is always fulfilled (in particular also at…
Numerical calculation of the combinatorial entropy of partially ordered ice
Bernd A. Berg, Wei Yang
Using a one-parameter case as an example, we demonstrate that multicanonical simulations allow for accurate estimates of the residual combinatorial entropy of partially ordered ice…
Rugged Metropolis Sampling with Simultaneous Updating of Two Dynamical Variables
Bernd A. Berg, Huan-Xiang Zhou
The Rugged Metropolis (RM) algorithm is a biased updating scheme, which aims at directly hitting the most likely configurations in a rugged free energy landscape. Details of the on…
Metropolis simulations of Met-Enkephalin with solvent-accessible area parameterizations
Bernd A. Berg, Hsiao-Ping Hsu
We investigate the solvent-accessible area method by means of Metropolis simulations of the brain peptide Met-Enkephalin at 300. For the energy function ECEPP/2 nine atomic sol…
Biased Metropolis Sampling for Rugged Free Energy Landscapes
Bernd A. Berg
Metropolis simulations of all-atom models of peptides (i.e. small proteins) are considered. Inspired by the funnel picture of Bryngelson and Wolyness, a transformation of the updat…
Multi-Overlap Simulations for Transitions between Reference Configurations
B. A. Berg, H. Noguchi, Y. Okamoto
We introduce a new procedure to construct weight factors, which flatten the probability density of the overlap with respect to some pre-defined reference configuration. This allows…