• TMSmesh

  • Referenced in 20 articles [sw14719]
  • numerical simulation of biomolecules, especially in implicit solvent modeling (e.g., see a review...
  • APBS

  • Referenced in 92 articles [sw05766]
  • most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media ... protein and protein-protein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding...
  • PyGBe

  • Referenced in 5 articles [sw17642]
  • model. It computes solvation energies for proteins modeled with any number of dielectric regions ... Poisson-Boltzmann equation of the implicit-solvent model in integral form. PyGBe achieves both algorithmic...
  • SDPBS

  • Referenced in 7 articles [sw17208]
  • equation (PBE) is one important implicit solvent continuum model for calculating electrostatics of protein...
  • LS-VISM

  • Referenced in 3 articles [sw16158]
  • implement numerical methods for a variational implicit-solvent model (VISM). The input of the package...
  • SIMS

  • Referenced in 2 articles [sw21778]
  • dielectric border between high dielectric solvent and the low dielectric molecular interior. The SIMS method ... used in a variety of implicit methods of modeling solvent effects. The SIMS program...
  • SELM

  • Referenced in 3 articles [sw17574]
  • dynamic thermostats to extend implicit-solvent coarse-grained (IS-CG) models by incorporating kinetic contributions...
  • NSOL

  • Referenced in 2 articles [sw21620]
  • included as implicit solvation effects, such as continuum model using distance dependent dielectric constant. While ... methods that calculate solvation energy using solvent accessible surface area; ASP (atomic solvation parameters) model...
  • OPM

  • Referenced in 2 articles [sw33426]
  • encourages open innovation and reproducible research for modeling and simulation of porous media processes ... fully implicit black-oil simulator that also supports solvent and polymer options. It is built...
  • ProFASi

  • Referenced in 1 article [sw30576]
  • simulations and analyzing the generated data. The model implemented uses an all-atom protein description ... degrees of freedom, and a simplified implicit solvent force field...
  • VASPsol

  • Referenced in 1 article [sw27046]
  • VASPsol: We implemented an implicit solvation model that describes the effect of electrostatics, cavitation ... interaction between a solute and solvent into the plane-wave DFT code VASP. Our implementation...
  • ADOL-C

  • Referenced in 249 articles [sw00019]
  • ADOL-C: Automatic Differentiation of C/C++. We present...
  • BoomerAMG

  • Referenced in 195 articles [sw00086]
  • BoomerAMG: A parallel algebraic multigrid solver and preconditioner...
  • hypre

  • Referenced in 306 articles [sw00426]
  • hypre is a software library for the solution...
  • LAPACK

  • Referenced in 1695 articles [sw00503]
  • LAPACK is written in Fortran 90 and provides...
  • Matlab

  • Referenced in 13460 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • UMFPACK

  • Referenced in 412 articles [sw00989]
  • An ANSI C code for sparse LU factorization...
  • ISIM

  • Referenced in 4 articles [sw01100]
  • SimTK ISIM interface a simple Java graphical user...
  • AMBER

  • Referenced in 57 articles [sw01333]
  • AmberTools is a set of programs for biomolecular...
  • ADIFOR

  • Referenced in 254 articles [sw02185]
  • ADIFOR is a tool for the automatic differentiation...