• VMD

  • Referenced in 51 articles [sw18651]
  • analyze the trajectory of a molecular dynamics (MD) simulation. In particular...
  • WIGGLE

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

  • Referenced in 4 articles [sw10227]
  • program package for classical molecular dynamics simulations (MD). A few capabilities of the package were...
  • ABINIT-MP

  • Referenced in 3 articles [sw10528]
  • program package for classical molecular dynamics simulations (MD). A few capabilities of the package were...
  • MOSCITO

  • Referenced in 1 article [sw04247]
  • dynamics (MD) simulation. Moscito is designed for condensed phase and gas phase MD simulations ... molecular aggregates. Standard molecular mechanics force-fields such as AMBER, OPLS, CHARMM and GROMOS...
  • MDAnalysis

  • Referenced in 1 article [sw17696]
  • structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures...
  • RUMD

  • Referenced in 1 article [sw19830]
  • general purpose, high-performance molecular dynamics (MD) simulation package running on graphical processing units...
  • MDGRAPE-4

  • Referenced in 0 articles [sw18544]
  • dynamics (MD) simulations. MDGRAPE-4 is designed to achieve strong scalability for protein MD simulations ... been improved, we plan to run MD simulations on MDGRAPE-4 in 2014. The MDGRAPE ... system will enable long-time molecular dynamics simulations of small systems. It is also useful...
  • pyPcazip

  • Referenced in 0 articles [sw20634]
  • timescales, the large generated amounts of molecular simulation data. In light of this, we have ... compression and analysis of molecular dynamics (MD) simulation data. The software is compatible with trajectory...
  • ProtoMD

  • Referenced in 0 articles [sw19021]
  • development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods...
  • MUPHY

  • Referenced in 8 articles [sw10447]
  • physics/scale code for high performance bio-fluidic simulations. We present a parallel version of MUPHY ... based upon the combination of microscopic Molecular Dynamics (MD) with a hydro-kinetic Lattice Boltzmann...
  • THOR

  • Referenced in 1 article [sw07915]
  • Classical Molecular Dynamics (MD) and Stochastic Molecular Dynamics Monte Carlo (MC) simulations, coupled to Embedded ... used in our molecular dynamic approach is to run the MD program simultaneously with ... code. During the dynamic process the MD routine call the SCF-DVM program to redefine ... this case, random molecular geometries are calculated and used by the Simulated Annealing Method...
  • M.DynaMix

  • Referenced in 3 articles [sw09596]
  • MD simulation package for arbitrary molecular mixtures. A general purpose, scalable parallel molecular dynamics package...
  • sPuReMD

  • Referenced in 3 articles [sw12865]
  • serial Purdue reactive molecular dynamics program), a unique reactive classical MD code. We describe various ... equilibration solver at the core of the simulation engine. This Krylov subspace solver relies...
  • PLUMED

  • Referenced in 2 articles [sw06050]
  • interfaced with the most popular classical molecular dynamics (MD) codes through a simple patching procedure ... exploit many different MD engines depending on the system simulated and on the computational resources...
  • LPMD

  • Referenced in 1 article [sw12495]
  • molecular dynamics (MD) code using interatomic potential functions. LPMD is able to perform equilibrium MD ... simulations of bulk crystalline solids, amorphous solids and liquids, as well as non-equilibrium...
  • HALMD

  • Referenced in 0 articles [sw17697]
  • MD package is a high-precision molecular dynamics package for large-scale simulations...
  • Maple

  • Referenced in 3967 articles [sw00545]
  • The result of over 30 years of cutting...
  • REACH

  • Referenced in 6 articles [sw00788]
  • REACH ( R ealistic E xtension A lgorithm via...
  • RESCUER

  • Referenced in 2 articles [sw03130]
  • The application of RESCUER software in effective MEMS...