• OpenMM

  • Referenced in 9 articles [sw19831]
  • OpenMM: A high performance toolkit for molecular simulation. Use it as a library...
  • PARSEC

  • Referenced in 20 articles [sw22333]
  • directions), or confined. Structural relaxation. Simulated annealing. Langevin molecular dynamics. Polarizability calculations (confined-system boundary...
  • ESPResSo

  • Referenced in 17 articles [sw06335]
  • performing and analyzing scientific Molecular Dynamics many-particle simulations of ”coarse-grained” bead-spring models ... physics, chemistry and molecular biology. It can be used to simulate systems such as polymers...
  • 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 ... calculating long-range forces in molecular simulations, incorporating a novel three-dimensional fast Fourier transform...
  • MDAnalysis

  • Referenced in 9 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...
  • DESMOND

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

  • Referenced in 8 articles [sw19829]
  • 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 ... well as for research projects in atomic, molecular and optical physics or in physical...
  • SETTLE

  • Referenced in 13 articles [sw12892]
  • mechanics and dynamics. Several series of molecular dynamics simulations were carried out to examine...
  • TMSmesh

  • Referenced in 21 articles [sw14719]
  • Trace Technique. Qualified, stable, and efficient molecular surface meshing appears to be necessitated by recent ... developments for realistic mathematical modeling and numerical simulation of biomolecules, especially in implicit solvent modeling ... paper, we present a new method: tracing molecular surface for meshing (TMSmesh) the Gaussian surface ... route to simulate electrostatic solvation of large-scale molecular systems. The binary version of TMSmesh...
  • 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...
  • DYANA

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

  • Referenced in 4 articles [sw23454]
  • Dynamics Code for Large Systems. The molecular dynamics simulation code ls1 mardyn is presented ... world record for the largest molecular simulation with over four trillion particles. It enables ... 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...
  • CP2K

  • Referenced in 8 articles [sw15391]
  • that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological ... fields (AMBER, CHARMM, …). CP2K can do simulations of molecular dynamics, metadynamics, Monte Carlo, Ehrenfest dynamics...
  • DynamO

  • Referenced in 6 articles [sw20352]
  • general event-driven molecular-dynamics simulator, Molecular-dynamics algorithms for systems of particles interacting through ... present DynamO, a general event-driven simulation package which displays the optimal O(N) asymptotic...
  • 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...
  • 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 ... modified form of the Beeman algorithm. Simulations may be performed in the usual NVE ensemble...
  • ASE

  • Referenced in 18 articles [sw30602]
  • performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints...
  • P-LINCS

  • Referenced in 3 articles [sw21733]
  • parallel linear constraint solver for molecular simulation. By removing the fastest degrees of freedom, constraints ... increase of the time step in molecular simulations. In the last decade parallel simulations have...
  • DeePMD-kit

  • Referenced in 3 articles [sw22318]
  • accuracy-versus-efficiency dilemma in molecular simulations. Here we describe DeePMD-kit, a package written ... energy and force field and to perform molecular dynamics. Potential applications of DeePMD-kit span ... used to perform efficient molecular simulations for different purposes. As an example of the many ... functional theory. We demonstrate that the resulted molecular dynamics model reproduces accurately the structural information...
  • IMD

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