• 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...
  • DynamO

  • Referenced in 6 articles [sw20352]
  • free O(N) general event-driven molecular-dynamics simulator, Molecular-dynamics algorithms for systems ... present DynamO, a general event-driven simulation package which displays the optimal O(N) asymptotic...
  • E-CELL

  • Referenced in 23 articles [sw07917]
  • build models for simulating intracellular molecular processes to predict the dynamic behavior of living cells ... Previous work in biochemical and genetic simulation has isolated well-characterized pathways for detailed analysis...
  • Moldy

  • Referenced in 5 articles [sw01311]
  • Moldy: a portable molecular dynamics simulation program for serial and parallel computers. Moldy ... highly portable C program for performing molecular-dynamics simulations of solids and liquids using periodic ... ions in any mixture. Molecules or molecular ions are treated in the rigid-molecule approximation...
  • IMD

  • Referenced in 7 articles [sw00438]
  • software package for classical molecular dynamics simulations. Several types of interactions are supported, such...
  • MarDyn

  • Referenced in 4 articles [sw23454]
  • Dynamics Code for Large Systems. The molecular dynamics simulation code ls1 mardyn is presented ... holds the world record for the largest molecular simulation with over four trillion particles ... were previously out of scope for molecular dynamics simulation. With an efficient dynamic load balancing ... interfaces, as well as nonequilibrium molecular dynamics simulation of heat and mass transfer...
  • ESPResSo

  • Referenced in 17 articles [sw06335]
  • performing and analyzing scientific Molecular Dynamics many-particle simulations of ”coarse-grained” bead-spring models ... soft-matter research in physics, chemistry and molecular biology. It can be used to simulate...
  • WIGGLE

  • Referenced in 10 articles [sw02594]
  • theory of conventional constrained molecular dynamics (MD) simulations is reexamined based on a projection operator...
  • REACH

  • Referenced in 6 articles [sw00788]
  • package for residue-scale coarse-grained biomolecular simulation. The program calculates the force constants ... variance–covariance matrix obtained from atomistic molecular dynamics simulation. Secondary-structure dependence of the force...
  • WavePacket

  • Referenced in 8 articles [sw19829]
  • numerical simulation of quantum-mechanical dynamics. It can be used to solve time-independent ... treated, which allows to simulate molecular quantum dynamics beyond the Born-Oppenheimer approximation. Optionally accounting ... dipole approximation, WavePacket can be used to simulate experiments involving tailored light pulses in photo ... chemistry.The graphical capabilities allow visualization of quantum dynamics ’on the fly’, including Wigner phase space...
  • ASE

  • Referenced in 17 articles [sw30602]
  • performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints...
  • CP2K

  • Referenced in 8 articles [sw15391]
  • AMBER, CHARMM, …). CP2K can do simulations of molecular dynamics, metadynamics, Monte Carlo, Ehrenfest dynamics, vibrational...
  • PuReMD

  • Referenced in 3 articles [sw18042]
  • PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs. We present an efficient ... community code, PuReMD, for reactive molecular dynamics simulations using the ReaxFF force field. PuReMD...
  • Qmd-plot

  • Referenced in 3 articles [sw10941]
  • data, developed in the context of molecular dynamics simulations. Qmd-plot is a utility ... rapid information about past or on-going simulations, or real-time data collections ... plots or as a function of simulated or real time. Time series records ... been developed in the context of molecular dynamics simulations. We give examples of time series...
  • PEACH

  • Referenced in 4 articles [sw10227]
  • biological molecules. A program package for molecular simulations of biological molecules was developed. The package ... ABINIT-MP, a program for the fragment molecular orbital (FMO) method [K. Kitaura ... PEACH, a program package for classical molecular dynamics simulations (MD). A few capabilities...
  • Ibisco

  • Referenced in 2 articles [sw14733]
  • molecular dynamics simulation package for coarse-grained simulation. BIsCO is a parallel molecular dynamics simulation ... package developed specially for coarse-grained simulations with numerical potentials derived by the iterative Boltzmann ... addition to common features of molecular dynamics programs, the techniques of dissipative particle dynamics (Groot ... coarse-graining. The reverse nonequilibrium molecular dynamics simulation method (Müller-Plathe, Phys...
  • GROMOS

  • Referenced in 30 articles [sw08091]
  • MOlecular Simulation computer program package, which has been developed since 1978 for the dynamic modelling...
  • i-pi

  • Referenced in 2 articles [sw22319]
  • interface for ab initio path integral molecular dynamics simulations. A Python interface for ab initio ... path integral molecular dynamics simulations. i-PI is composed of a Python server...
  • ABINIT-MP

  • Referenced in 3 articles [sw10528]
  • biological molecules. A program package for molecular simulations of biological molecules was developed. The package ... ABINIT-MP, a program for the fragment molecular orbital (FMO) method [{it K. Kitaura ... PEACH, a program package for classical molecular dynamics simulations (MD). A few capabilities...
  • Pwpaw

  • Referenced in 3 articles [sw26737]
  • capabilities, including structural geometry optimization and molecular dynamics simulations within the Born-Oppenheimer approximation...