
Gromacs
 Referenced in 81 articles
[sw04128]
 versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems...

APBS
 Referenced in 72 articles
[sw05766]
 proteinprotein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations...

NAMD
 Referenced in 61 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...

VMD
 Referenced in 55 articles
[sw18651]
 analyze the trajectory of a molecular dynamics (MD) simulation. In particular...

NAMD2
 Referenced in 19 articles
[sw09642]
 NAMD2: Greater scalability for parallel molecular dynamics. Molecular dynamics programs simulate the behavior of biomolecular...

LAMMPS
 Referenced in 30 articles
[sw05952]
 Massively Parallel Simulator) is a classical molecular dynamics code. LAMMPS can model an ensemble...

ABINIT
 Referenced in 27 articles
[sw06111]
 forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate...

DL_POLY
 Referenced in 24 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...

NWChem
 Referenced in 24 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...

GSHMC
 Referenced in 13 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...

STAPL
 Referenced in 13 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...

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

SIESTA
 Referenced in 17 articles
[sw05949]
 electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. SIESTA...

GULP
 Referenced in 15 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...

PLUMP
 Referenced in 14 articles
[sw00718]
 dynamic aspects, namely a tight binding molecular dynamics code and a finite element package. Finally...

Packmol
 Referenced in 9 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...

WIGGLE
 Referenced in 10 articles
[sw02594]
 WIGGLE: a new constrained molecular dynamics algorithm in Cartesian coordinate. The theory of conventional constrained ... molecular dynamics (MD) simulations is reexamined based on a projection operator approach. A new algorithm...

PARSEC
 Referenced in 14 articles
[sw22333]
 confined. Structural relaxation. Simulated annealing. Langevin molecular dynamics. Polarizability calculations (confinedsystem boundary conditions only...

ProtoMol
 Referenced in 8 articles
[sw10728]
 framework for prototyping novel algorithms for molecular dynamics. ProtoMol is a highperformance framework ... rapid prototyping of novel algorithms for molecular dynamics and related applications. Its flexibility is achieved ... domain analysis of numerical integrators for molecular dynamics (MD) and of fast solvers...

SETTLE
 Referenced in 10 articles
[sw12892]
 mechanics and dynamics. Several series of molecular dynamics simulations were carried out to examine...