
Gromacs
 Referenced in 120 articles
[sw04128]
 versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems...

APBS
 Referenced in 88 articles
[sw05766]
 proteinprotein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations...

VMD
 Referenced in 83 articles
[sw18651]
 analyze the trajectory of a molecular dynamics (MD) simulation. In particular...

NAMD
 Referenced in 78 articles
[sw03198]
 NAMD is a parallel molecular dynamics code designed for highperformance simulation of large biomolecular ... using gigabit ethernet. NAMD uses the popular molecular graphics program VMD for simulation setup...

LAMMPS
 Referenced in 59 articles
[sw05952]
 Massively Parallel Simulator) is a classical molecular dynamics code. LAMMPS can model an ensemble...

ABINIT
 Referenced in 46 articles
[sw06111]
 forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate...

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

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

DL_POLY
 Referenced in 31 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...

GSHMC
 Referenced in 16 articles
[sw02631]
 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 highorder along molecular dynamics trajectories. The modified energy is based on backward...

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

STAPL
 Referenced in 14 articles
[sw00910]
 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...

GULP
 Referenced in 18 articles
[sw01459]
 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...

Packmol
 Referenced in 12 articles
[sw13408]
 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 stateoftheart molecular dynamics systems varies from a few seconds...

PARSEC
 Referenced in 19 articles
[sw22333]
 confined. Structural relaxation. Simulated annealing. Langevin molecular dynamics. Polarizability calculations (confinedsystem boundary conditions only...

UNICORE
 Referenced in 17 articles
[sw02295]
 existing applications into UNICORE. CarParrinello Molecular Dynamics (CPMD) application is used as an example...

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

MUPHY
 Referenced in 16 articles
[sw10447]
 based upon the combination of microscopic Molecular Dynamics (MD) with a hydrokinetic Lattice Boltzmann...

LIGGGHTS
 Referenced in 11 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...

ESPResSo
 Referenced in 15 articles
[sw06335]
 package for performing and analyzing scientific Molecular Dynamics manyparticle simulations of ”coarsegrained” bead ... softmatter research in physics, chemistry and molecular biology. It can be used to simulate...