• Gromacs

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

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

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

  • Referenced in 65 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 79 articles [sw03198]
  • parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based ... using gigabit ethernet. NAMD uses the popular molecular graphics program VMD for simulation setup...
  • Packmol

  • Referenced in 13 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 state-of-the-art 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 high-order along molecular dynamics trajectories. The modified energy is based on backward...
  • NWChem

  • Referenced in 39 articles [sw06127]
  • NWChem also performs classical molecular dynamics and free energy simulations. These approaches may be combined ... perform mixed quantum-mechanics and molecular-mechanics simulations. Developed at Pacific Northwest National Laboratory, NWChem...
  • VAMPnets

  • Referenced in 14 articles [sw32927]
  • protein-drug binding, from high-throughput molecular dynamics simulations. Current methods employ transformation of simulated ... related model of the interconversion rates between molecular structures. This handcrafted approach demands a substantial...
  • 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 ... platform for DEM simulations. LAMMPS offers a GRANULAR package to perform these kind of simulations...
  • DESMOND

  • Referenced in 13 articles [sw06114]
  • Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional computer...
  • 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...
  • DYANA

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

  • Referenced in 8 articles [sw17696]
  • toolkit for the analysis of molecular dynamics simulations. MDAnalysis is an object-oriented library ... structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures...
  • 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 production-class biomolecular dynamics ... microsecond-long trajectory for an all-atom molecular system in explicit TIP3P water...
  • APBS

  • Referenced in 91 articles [sw05766]
  • several areas of biomolecular simulation, including simulation of diffusional processes to determine ligand-protein ... protein-protein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations...
  • DL_POLY_3

  • Referenced in 6 articles [sw09141]
  • CCP5 national UK code for molecular-dynamics simulations. DL_POLY_3 is a general-purpose ... molecular-dynamics simulation package embedding a highly efficient domain decomposition (DD) parallelization strategy ... method for calculating long-range forces in molecular simulations, incorporating a novel three-dimensional fast...