Molecular dynamics, monte carlo simulations, and langevin dynamics: a computational review
Macromolecular structures, such as neuraminidases, hemagglutinins, and monoclonal
antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is …
antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is …
Modeling nucleic acids
Nucleic acids are an important class of biological macromolecules that carry out a variety of
cellular roles. For many functions, naturally occurring DNA and RNA molecules need to fold …
cellular roles. For many functions, naturally occurring DNA and RNA molecules need to fold …
A nucleotide-level coarse-grained model of RNA
We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining
methodology recently developed for the oxDNA model of DNA. The model is designed to …
methodology recently developed for the oxDNA model of DNA. The model is designed to …
Efficient and direct generation of multidimensional free energy surfaces via adiabatic dynamics without coordinate transformations
Adiabatic free energy dynamics (AFED) was introduced by Rosso et al.[J. Chem. Phys.
2002, 116, 4389] for computing free energy profiles quickly and accurately using a …
2002, 116, 4389] for computing free energy profiles quickly and accurately using a …
A self-learning algorithm for biased molecular dynamics
A new self-learning algorithm for accelerated dynamics, reconnaissance metadynamics, is
proposed that is able to work with a very large number of collective coordinates …
proposed that is able to work with a very large number of collective coordinates …
Using the local elevation method to construct optimized umbrella sampling potentials: calculation of the relative free energies and interconversion barriers of …
HS Hansen, PH Hünenberger - Journal of computational …, 2010 - Wiley Online Library
A method is proposed to combine the local elevation (LE) conformational searching and the
umbrella sampling (US) conformational sampling approaches into a single local elevation …
umbrella sampling (US) conformational sampling approaches into a single local elevation …
Heating and flooding: A unified approach for rapid generation of free energy surfaces
We propose a general framework for the efficient sampling of conformational equilibria in
complex systems and the generation of associated free energy hypersurfaces in terms of a …
complex systems and the generation of associated free energy hypersurfaces in terms of a …
Free energy reconstruction from metadynamics or adiabatic free energy dynamics simulations
In molecular dynamics simulations, most enhanced sampling methods are traditionally
associated with one particular estimator to calculate the free energy surface (FES), such as …
associated with one particular estimator to calculate the free energy surface (FES), such as …
Stochastic, resonance-free multiple time-step algorithm for molecular dynamics with very large time steps
Molecular dynamics is one of the most commonly used approaches for studying the
dynamics and statistical distributions of physical, chemical, and biological systems using …
dynamics and statistical distributions of physical, chemical, and biological systems using …
[HTML][HTML] Molecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules
T Schlick - F1000 biology reports, 2009 - ncbi.nlm.nih.gov
The rugged energy landscape of biomolecules together with shortcomings of traditional
molecular dynamics (MD) simulations require specialized methods for capturing large-scale …
molecular dynamics (MD) simulations require specialized methods for capturing large-scale …