Convergence and error estimation in free energy calculations using the weighted histogram analysis method
F Zhu, G Hummer - Journal of computational chemistry, 2012 - Wiley Online Library
The weighted histogram analysis method (WHAM) has become the standard technique for
the analysis of umbrella sampling simulations. In this article, we address the challenges (1) …
the analysis of umbrella sampling simulations. In this article, we address the challenges (1) …
Generic coarse-grained model for protein folding and aggregation
Groningen University, Groningen, Netherlands. MARTINI force field: extension to
carbohydrates We present an extension of the coarse grained (CG) MARTINI force field (1) …
carbohydrates We present an extension of the coarse grained (CG) MARTINI force field (1) …
Automated parametrization of the coarse-grained Martini force field for small organic molecules
The systematic exploration of chemical compound space holds many promises toward
structure–function relationships and material design. In the context of computer simulations …
structure–function relationships and material design. In the context of computer simulations …
Drug–membrane permeability across chemical space
Unraveling the relation between the chemical structure of small druglike compounds and
their rate of passive permeation across lipid membranes is of fundamental importance for …
their rate of passive permeation across lipid membranes is of fundamental importance for …
[HTML][HTML] Folding and insertion thermodynamics of the transmembrane WALP peptide
The anchor of most integral membrane proteins consists of one or several helices spanning
the lipid bilayer. The WALP peptide, GWW (LA) n (L) WWA, is a common model helix to …
the lipid bilayer. The WALP peptide, GWW (LA) n (L) WWA, is a common model helix to …
A coarse-grained thermodynamic model for the predictive engineering of valence-selective membranes
Membrane-based filtration has shown promise in the treatment of municipal and industrial
water supplies. Most existing filtration membranes rely on size-selective rejection …
water supplies. Most existing filtration membranes rely on size-selective rejection …
In silico screening of drug-membrane thermodynamics reveals linear relations between bulk partitioning and the potential of mean force
The partitioning of small molecules in cell membranes—a key parameter for pharmaceutical
applications—typically relies on experimentally available bulk partitioning coefficients …
applications—typically relies on experimentally available bulk partitioning coefficients …
More than the sum of its parts: Coarse-grained peptide-lipid interactions from a simple cross-parametrization
Interfacial systems are at the core of fascinating phenomena in many disciplines, such as
biochemistry, soft-matter physics, and food science. However, the parametrization of …
biochemistry, soft-matter physics, and food science. However, the parametrization of …
Monte Carlo simulations in statistical physics—From basic principles to advanced applications
W Janke - Order, Disorder and Criticality: Advanced Problems of …, 2013 - World Scientific
This chapter starts with an overview of Monte Carlo computer simulation methodologies
which are illustrated for the simple case of the Ising model. After reviewing importance …
which are illustrated for the simple case of the Ising model. After reviewing importance …
[HTML][HTML] Communication: Iteration-free, weighted histogram analysis method in terms of intensive variables
We present an iteration-free weighted histogram method in terms of intensive variables that
directly determines the inverse statistical temperature, β S=∂ S/∂ E, with S the …
directly determines the inverse statistical temperature, β S=∂ S/∂ E, with S the …