Computer simulation of molecular dynamics: methodology, applications, and perspectives in chemistry
WF Van Gunsteren… - … International Edition in …, 1990 - Wiley Online Library
During recent decades it has become feasible to simulate the dynamics of molecular
systems on a computer. The method of molecular dynamics (MD) solves Newton's equations …
systems on a computer. The method of molecular dynamics (MD) solves Newton's equations …
Thermostat algorithms for molecular dynamics simulations
PH Hünenberger - Advanced computer simulation: Approaches for soft …, 2005 - Springer
Molecular dynamics simulations rely on integrating the classical (Newtonian) equations of
motion for a molecular system and thus, sample a microcanonical (constant-energy) …
motion for a molecular system and thus, sample a microcanonical (constant-energy) …
CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field
Proper treatment of nonbonded interactions is essential for the accuracy of molecular
dynamics (MD) simulations, especially in studies of lipid mono-and bilayers. The use of the …
dynamics (MD) simulations, especially in studies of lipid mono-and bilayers. The use of the …
g_mmpbsaA GROMACS Tool for High-Throughput MM-PBSA Calculations
Molecular mechanics Poisson–Boltzmann surface area (MM-PBSA), a method to estimate
interaction free energies, has been increasingly used in the study of biomolecular …
interaction free energies, has been increasingly used in the study of biomolecular …
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
Motivation: Molecular simulation has historically been a low-throughput technique, but faster
computers and increasing amounts of genomic and structural data are changing this by …
computers and increasing amounts of genomic and structural data are changing this by …
Structure of SARS-CoV-2 membrane protein essential for virus assembly
Z Zhang, N Nomura, Y Muramoto, T Ekimoto… - Nature …, 2022 - nature.com
The coronavirus membrane protein (M) is the most abundant viral structural protein and
plays a central role in virus assembly and morphogenesis. However, the process of M …
plays a central role in virus assembly and morphogenesis. However, the process of M …
Nirmatrelvir-resistant SARS-CoV-2 variants with high fitness in an infectious cell culture system
Y Zhou, KA Gammeltoft, LA Ryberg, LV Pham… - Science …, 2022 - science.org
The oral protease inhibitor nirmatrelvir is of key importance for prevention of severe
coronavirus disease 2019 (COVID-19). To facilitate resistance monitoring, we studied …
coronavirus disease 2019 (COVID-19). To facilitate resistance monitoring, we studied …
[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 …
A smooth particle mesh Ewald method
U Essmann, L Perera, ML Berkowitz… - The Journal of …, 1995 - pubs.aip.org
The previously developed particle mesh Ewald method is reformulated in terms of efficient B‐
spline interpolation of the structure factors. This reformulation allows a natural extension of …
spline interpolation of the structure factors. This reformulation allows a natural extension of …