[HTML][HTML] Classical and reactive molecular dynamics: Principles and applications in combustion and energy systems
Molecular dynamics (MD) has evolved into a ubiquitous, versatile and powerful
computational method for fundamental research in science branches such as biology …
computational method for fundamental research in science branches such as biology …
An empirical polarizable force field based on the classical drude oscillator model: development history and recent applications
Molecular mechanics force fields that explicitly account for induced polarization represent
the next generation of physical models for molecular dynamics simulations. Several …
the next generation of physical models for molecular dynamics simulations. Several …
PhysNet: A neural network for predicting energies, forces, dipole moments, and partial charges
In recent years, machine learning (ML) methods have become increasingly popular in
computational chemistry. After being trained on appropriate ab initio reference data, these …
computational chemistry. After being trained on appropriate ab initio reference data, these …
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 …
Developing a fully glycosylated full-length SARS-CoV-2 spike protein model in a viral membrane
This technical study describes all-atom modeling and simulation of a fully glycosylated full-
length SARS-CoV-2 spike (S) protein in a viral membrane. First, starting from PDB: 6VSB …
length SARS-CoV-2 spike (S) protein in a viral membrane. First, starting from PDB: 6VSB …
Improving protein-ligand docking results with high-throughput molecular dynamics simulations
H Guterres, W Im - Journal of chemical information and modeling, 2020 - ACS Publications
Structure-based virtual screening relies on classical scoring functions that often fail to
reliably discriminate binders from nonbinders. In this work, we present a high-throughput …
reliably discriminate binders from nonbinders. In this work, we present a high-throughput …
CHARMM‐GUI Membrane Builder toward realistic biological membrane simulations
CHARMM‐GUI Membrane Builder, http://www. charmm‐gui. org/input/membrane, is a web‐
based user interface designed to interactively build all‐atom protein/membrane or …
based user interface designed to interactively build all‐atom protein/membrane or …
CHARMM-GUI nanomaterial modeler for modeling and simulation of nanomaterial systems
Molecular modeling and simulation are invaluable tools for nanoscience that predict
mechanical, physicochemical, and thermodynamic properties of nanomaterials and provide …
mechanical, physicochemical, and thermodynamic properties of nanomaterials and provide …
CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates
Characterizing glycans and glycoconjugates in the context of three-dimensional structures is
important in understanding their biological roles and developing efficient therapeutic agents …
important in understanding their biological roles and developing efficient therapeutic agents …
Modeling molecular interactions in water: From pairwise to many-body potential energy functions
Almost 50 years have passed from the first computer simulations of water, and a large
number of molecular models have been proposed since then to elucidate the unique …
number of molecular models have been proposed since then to elucidate the unique …