
Gromacs
 Referenced in 115 articles
[sw04128]
 versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems...

VMD
 Referenced in 84 articles
[sw18651]
 analyze the trajectory of a molecular dynamics (MD) simulation. In particular...

ABINIT
 Referenced in 45 articles
[sw06111]
 forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate...

DL_POLY
 Referenced in 30 articles
[sw09140]
 POLY is a generalpurpose molecular dynamics simulation package, which was developed by Daresbury Laboratory ... 1990s for the molecular simulation community in the United Kingdom. The package...

LAMMPS
 Referenced in 56 articles
[sw05952]
 scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics code. LAMMPS can model...

SIESTA
 Referenced in 22 articles
[sw05949]
 electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. SIESTA...

NAMD
 Referenced in 77 articles
[sw03198]
 parallel molecular dynamics code designed for highperformance simulation of large biomolecular systems. Based ... using gigabit ethernet. NAMD uses the popular molecular graphics program VMD for simulation setup...

Packmol
 Referenced in 12 articles
[sw13408]
 package for building initial configurations for molecular dynamics simulations. Adequate initial configurations for molecular dynamics ... overall structure. In order that the simulations are not disrupted by large van der Waals ... keep safe pairwise distances. Obtaining such a molecular arrangement can be considered a packing problem ... time for stateoftheart molecular dynamics systems varies from a few seconds...

GSHMC
 Referenced in 16 articles
[sw02631]
 method is based on classical molecular dynamics simulations combined with a Metropolis acceptance criterion ... similar to stochastic Langevin and Brownian dynamics simulations. It is, however, ultimate to the success ... that the rejection rate in the molecular dynamics part is kept at a minimum. Otherwise ... preserved to highorder along molecular dynamics trajectories. The modified energy is based on backward...

NWChem
 Referenced in 38 articles
[sw06127]
 NWChem also performs classical molecular dynamics and free energy simulations. These approaches may be combined ... perform mixed quantummechanics and molecularmechanics simulations. Developed at Pacific Northwest National Laboratory, NWChem...

NAMD2
 Referenced in 21 articles
[sw09642]
 scalability for parallel molecular dynamics. Molecular dynamics programs simulate the behavior of biomolecular systems, leading...

SETTLE
 Referenced in 13 articles
[sw12892]
 mechanics and dynamics. Several series of molecular dynamics simulations were carried out to examine...

LIGGGHTS
 Referenced in 10 articles
[sw18119]
 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 ... platform for DEM simulations. LAMMPS offers a GRANULAR package to perform these kind of simulations...

DESMOND
 Referenced in 12 articles
[sw06114]
 Shaw Research to perform highspeed molecular dynamics simulations of biological systems on conventional computer...

DYANA
 Referenced in 11 articles
[sw08628]
 calculations. Torsion angle dynamics (TAD) performs molecular dynamics simulation using torsion angles instead of Cartesian...

ACEMD
 Referenced in 7 articles
[sw21783]
 ACEMD: Accelerated molecular dynamics simulations in the microseconds timescale. The high arithmetic performance and intrinsic ... offer a technological edge for molecular dynamics simulations. ACEMD is a productionclass biomolecular dynamics ... microsecondlong trajectory for an allatom molecular system in explicit TIP3P water...

VAMPnets
 Referenced in 9 articles
[sw32927]
 proteindrug binding, from highthroughput molecular dynamics simulations. Current methods employ transformation of simulated ... related model of the interconversion rates between molecular structures. This handcrafted approach demands a substantial...

APBS
 Referenced in 88 articles
[sw05766]
 several areas of biomolecular simulation, including simulation of diffusional processes to determine ligandprotein ... proteinprotein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations...

DynamO
 Referenced in 6 articles
[sw20352]
 free O(N) general eventdriven moleculardynamics simulator, Moleculardynamics algorithms for systems ... present DynamO, a general eventdriven simulation package which displays the optimal O(N) asymptotic...

PARSEC
 Referenced in 19 articles
[sw22333]
 directions), or confined. Structural relaxation. Simulated annealing. Langevin molecular dynamics. Polarizability calculations (confinedsystem boundary...