• Gromacs

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

  • Referenced in 28 articles [sw09140]
  • POLY: Application to molecular simulation. DL - POLY is a general-purpose molecular dynamics simulation package ... 1990s for the molecular simulation community in the United Kingdom. The package ... applications in many areas of molecular simulation. In this article we briefly review the history ... liquids and solutions; spectroscopy; ionic solids; molecular crystals; polymers; glasses; membranes; proteins; solid and liquid...
  • VMD

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

  • Referenced in 77 articles [sw03198]
  • parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based ... NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis...
  • LINCS

  • Referenced in 25 articles [sw08880]
  • LINCS: a linear constraint solver for molecular simulations. In this chapter we present ... LINear Constraint Solver (LINCS) for molecular simulations with bond constraints. The algorithm is inherently stable...
  • GROMOS

  • Referenced in 30 articles [sw08091]
  • acronym of the GROningen MOlecular Simulation computer program package, which has been developed since...
  • NWChem

  • Referenced in 36 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...
  • ABINIT

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

  • Referenced in 30 articles [sw08310]
  • application for the Monte Carlo simulation of molecular sequence evolution along phylogenetic trees ... program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny ... substitution process. A range of models of molecular evolution are implemented including the general reversible ... simulator that incorporates most of the commonly used (and computationally tractable) models of molecular sequence...
  • LAMMPS

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

  • Referenced in 16 articles [sw02631]
  • GSHMC: An efficient method for molecular simulation. The hybrid Monte Carlo (HMC) method ... 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 ... method that the rejection rate in the molecular dynamics part is kept at a minimum...
  • E-CELL

  • Referenced in 22 articles [sw07917]
  • CELL: software environment for whole-cell simulation. MOTIVATION: Genome sequencing projects and further systematic functional ... sets are producing an unprecedented mass of molecular information for a wide range of model ... begin to build models for simulating intracellular molecular processes to predict the dynamic behavior ... cells. Previous work in biochemical and genetic simulation has isolated well-characterized pathways for detailed...
  • APBS

  • Referenced in 87 articles [sw05766]
  • continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics ... important role in several areas of biomolecular simulation, including simulation of diffusional processes to determine ... protein-protein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations...
  • SIESTA

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

  • Referenced in 9 articles [sw26798]
  • Open Source program library for molecular simulation applications. In addition to providing ready ... standard and non-standard problems in molecular simulations...
  • 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...
  • SMMP

  • Referenced in 12 articles [sw00882]
  • Proteins) package is designed for molecular simulation of linear proteins using torsion angles as internal...
  • NAMD2

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

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