Basic ingredients of free energy calculations: a review
Methods to compute free energy differences between different states of a molecular system
are reviewed with the aim of identifying their basic ingredients and their utility when applied …
are reviewed with the aim of identifying their basic ingredients and their utility when applied …
[HTML][HTML] Comparison of silver and molybdenum microfocus X-ray sources for single-crystal structure determination
The quality of diffraction data obtained using silver and molybdenum microsources has been
compared for six model compounds with a wide range of absorption factors. The …
compared for six model compounds with a wide range of absorption factors. The …
Investigation of membrane fouling phenomenon using molecular dynamics simulations: A review
Membrane fouling remains a tremendous obstacle in the implementation of membrane
technology, which has motivated the use of a wide range of experimental techniques to …
technology, which has motivated the use of a wide range of experimental techniques to …
[HTML][HTML] The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA
Abstract The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA-binding protein
critical for viral genome packaging, yet the molecular details that underlie this process are …
critical for viral genome packaging, yet the molecular details that underlie this process are …
[HTML][HTML] A suite of tutorials for the WESTPA rare-events sampling software [Article v1. 0]
The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in
generating pathways and rate constants for rare events such as protein folding and protein …
generating pathways and rate constants for rare events such as protein folding and protein …
GROMACS: fast, flexible, and free
This article describes the software suite GROMACS (Groningen MAchine for Chemical
Simulation) that was developed at the University of Groningen, The Netherlands, in the early …
Simulation) that was developed at the University of Groningen, The Netherlands, in the early …
GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation
Molecular simulation is an extremely useful, but computationally very expensive tool for
studies of chemical and biomolecular systems. Here, we present a new implementation of …
studies of chemical and biomolecular systems. Here, we present a new implementation of …
GROMACS 3.0: a package for molecular simulation and trajectory analysis
GROMACS 3.0 is the latest release of a versatile and very well optimized package for
molecular simulation. Much effort has been devoted to achieving extremely high …
molecular simulation. Much effort has been devoted to achieving extremely high …
P-LINCS: A parallel linear constraint solver for molecular simulation
B Hess - Journal of chemical theory and computation, 2008 - ACS Publications
By removing the fastest degrees of freedom, constraints allow for an increase of the time
step in molecular simulations. In the last decade parallel simulations have become …
step in molecular simulations. In the last decade parallel simulations have become …
Long-time-step molecular dynamics through hydrogen mass repartitioning
Previous studies have shown that the method of hydrogen mass repartitioning (HMR) is a
potentially useful tool for accelerating molecular dynamics (MD) simulations. By …
potentially useful tool for accelerating molecular dynamics (MD) simulations. By …