• Gromacs

  • Referenced in 122 articles [sw04128]
  • versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems...
  • APBS

  • Referenced in 91 articles [sw05766]
  • protein-protein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations...
  • VMD

  • Referenced in 86 articles [sw18651]
  • analyze the trajectory of a molecular dynamics (MD) simulation. In particular...
  • NAMD

  • Referenced in 79 articles [sw03198]
  • 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...
  • LAMMPS

  • Referenced in 65 articles [sw05952]
  • Massively Parallel Simulator) is a classical molecular dynamics code. LAMMPS can model an ensemble...
  • ABINIT

  • Referenced in 47 articles [sw06111]
  • forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate...
  • NWChem

  • Referenced in 39 articles [sw06127]
  • 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...
  • 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 general-purpose 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 high-order along molecular dynamics trajectories. The modified energy is based on backward...
  • GULP

  • Referenced in 20 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...
  • SIESTA

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

  • Referenced in 13 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 state-of-the-art molecular dynamics systems varies from a few seconds...
  • 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...
  • PARSEC

  • Referenced in 19 articles [sw22333]
  • confined. Structural relaxation. Simulated annealing. Langevin molecular dynamics. Polarizability calculations (confined-system boundary conditions only...
  • ESPResSo

  • Referenced in 17 articles [sw06335]
  • 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...
  • UNICORE

  • Referenced in 17 articles [sw02295]
  • existing applications into UNICORE. Car-Parrinello 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 hydro-kinetic 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...