16 citations · 16 across the 2 of their papers we have counts for
6 papers
Protein simulations combining an all-atom force field with a Go term
Jan H Meinke, Ulrich H E Hansmann
Using a variant of parallel tempering, we study the changes in sampling within a simulation when the all-atom model is coupled to a Go-like potential. We find that the native struc…
Side chain and backbone ordering in a polypeptide
Y. Wei, W. Nadler, U. H. E. Hansmann
We report results from multicanonical simulations of polyglutamic acid chains of length of ten residues. For this simple polypeptide we observe a decoupling of backbone and side-ch…
On the Helix-coil Transition in Alanine-based Polypeptides in Gas Phase
Y. Wei, W. Nadler, U. H. E. Hansmann
Using multicanonical simulations, the authors study the effect of charged end groups on helix formation in alanine based polypeptides. They confirm earlier reports that neutral pol…
On Dynamics and Optimal Number of Replicas in Parallel Tempering Simulations
Walter Nadler, Ulrich H. E. Hansmann
We study the dynamics of parallel tempering simulations, also known as the replica exchange technique, which has become the method of choice for simulation of proteins and other co…
Optimizing Replica Exchange Moves For Molecular Dynamics
Walter Nadler, Ulrich H. E. Hansmann
In this short note we sketch the statistical physics framework of the replica exchange technique when applied to molecular dynamics simulations. In particular, we draw attention to…
Side-chain and backbone ordering in Homopolymers
Yanjie Wei, Walter Nadler, Ulrich H. E. Hansmann
In order to study the relation between backbone and side chain ordering in proteins, we have performed multicanonical simulations of deka-peptide chains with various side groups. G…