- Referenced in 121 articles
- versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems...
- Referenced in 88 articles
- protein-protein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations...
- Referenced in 84 articles
- analyze the trajectory of a molecular dynamics (MD) simulation. In particular...
- Referenced in 78 articles
- NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular ... using gigabit ethernet. NAMD uses the popular molecular graphics program VMD for simulation setup...
- Referenced in 60 articles
- Massively Parallel Simulator) is a classical molecular dynamics code. LAMMPS can model an ensemble...
- Referenced in 46 articles
- forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate...
- Referenced in 39 articles
- density. NWChem also performs classical molecular dynamics and free energy simulations. These approaches ... combined to perform mixed quantum-mechanics and molecular-mechanics simulations. Developed at Pacific Northwest National...
- Referenced in 21 articles
- NAMD2: Greater scalability for parallel molecular dynamics. Molecular dynamics programs simulate the behavior of biomolecular...
- Referenced in 31 articles
- POLY is a general-purpose molecular dynamics simulation package, which was developed by Daresbury Laboratory ... 1990s for the molecular simulation community in the United Kingdom. The package...
- Referenced in 16 articles
- method is based on classical molecular dynamics simulations combined with a Metropolis acceptance criterion ... process similar to stochastic Langevin and Brownian dynamics simulations. It is, however, ultimate ... that the rejection rate in the molecular dynamics part is kept at a minimum. Otherwise ... preserved to high-order along molecular dynamics trajectories. The modified energy is based on backward...
- Referenced in 20 articles
- dynamics, where possible, rather than on molecular dynamics. A variety of force fields ... spanning the shell model for ionic materials, molecular mechanics for organic systems, the embedded atom...
- Referenced in 22 articles
- electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. SIESTA...
- Referenced in 14 articles
- structures such as particle transport calculations, molecular dynamics, geometric modeling, and graph algorithms. STAPL provides ... results obtained using STAPL for a molecular dynamics code and a particle transport code...
- Referenced in 12 articles
- package for building initial configurations for molecular dynamics simulations. Adequate initial configurations for molecular dynamics ... keep safe pairwise distances. Obtaining such a molecular arrangement can be considered a packing problem ... time for state-of-the-art molecular dynamics systems varies from a few seconds...
- Referenced in 19 articles
- confined. Structural relaxation. Simulated annealing. Langevin molecular dynamics. Polarizability calculations (confined-system boundary conditions only...
- Referenced in 17 articles
- existing applications into UNICORE. Car-Parrinello Molecular Dynamics (CPMD) application is used as an example...
- Referenced in 13 articles
- mechanics and dynamics. Several series of molecular dynamics simulations were carried out to examine...
- Referenced in 16 articles
- based upon the combination of microscopic Molecular Dynamics (MD) with a hydro-kinetic Lattice Boltzmann...
- Referenced in 11 articles
- transfer simulations. LAMMPS is a classical molecular dynamics simulator. It is widely used ... field of Molecular Dynamics. Thanks to physical and algorithmic analogies, LAMMPS is a very good...
- Referenced in 15 articles
- package for performing and analyzing scientific Molecular Dynamics many-particle simulations of ”coarse-grained” bead ... soft-matter research in physics, chemistry and molecular biology. It can be used to simulate...