• CHARMM

  • Referenced in 115 articles [sw05953]
  • CHARMM (Chemistry at HARvard Macromolecular Mechanics). CHARMM models the dynamics and mechanics of macromolecular systems ... empirical and mixed empirical/quantum mechanical force fields. CHARMM is designed to investigate the structure...
  • NAMD

  • Referenced in 77 articles [sw03198]
  • also file-compatible with AMBER, CHARMM, and X-PLOR. NAMD is distributed free of charge...
  • PBEQ-Solver

  • Referenced in 13 articles [sw17203]
  • PBEQ module in the biomolecular simulation program CHARMM to solve the finite-difference PB equation ... visualization software, a Java applet integrated within CHARMM-GUI (http://www.charmm-gui.org). To reduce the computational...
  • MDAnalysis

  • Referenced in 7 articles [sw17696]
  • common file formats of simulation packages including CHARMM, Gromacs, Amber, and NAMD and the Protein ... selected with a syntax similar to CHARMM’s powerful selection commands. MDAnalysis enables both novice...
  • TINKER

  • Referenced in 10 articles [sw04095]
  • Amber (ff94, ff96, ff98, ff99, ff99SB), CHARMM (19, 22, 22/CMAP), Allinger...
  • CP2K

  • Referenced in 8 articles [sw15391]
  • MNDO, …), and classical force fields (AMBER, CHARMM, …). CP2K can do simulations of molecular dynamics, metadynamics...
  • ACEMD

  • Referenced in 7 articles [sw21783]
  • production-class biomolecular dynamics (MD) engine supporting CHARMM and AMBER force fields. Designed specifically...
  • CHARMM-GUI

  • Referenced in 2 articles [sw21732]
  • CHARMM-GUI: a web-based graphical user interface for CHARMM. CHARMM-GUI provides ... common and advanced simulation techniques. Currently, CHARMM-GUI supports CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS ... CHARMM/OpenMM simulation programs mostly based on the CHARMM force fields. CHARMM-GUI is powered ... CHARMM, an academic research program used world-wide for macromolecular dynamics and mechanics (http://www.charmm.org...
  • LOOPER

  • Referenced in 1 article [sw17376]
  • step algorithm (developed as a set of CHARMm scripts) and uses standard CHARMm force field ... final ranking stage based on the CHARMm energy with a generalized Born solvation term...
  • ACPYPE

  • Referenced in 2 articles [sw23579]
  • variety of molecular dynamics programmes like GROMACS, CHARMM and CNS. It is written...
  • Cassandra

  • Referenced in 2 articles [sw27542]
  • harmonic bond angles and improper angles, a CHARMM or OPLS-style dihedral potential, a Lennard...
  • CPPTRAJ

  • Referenced in 2 articles [sw33212]
  • many popular MD software packages including Amber, CHARMM, Gromacs, and NAMD. CPPTRAJ is also distributed...
  • MOSCITO

  • Referenced in 1 article [sw04247]
  • mechanics force-fields such as AMBER, OPLS, CHARMM and GROMOS can be employed. Simulations...
  • TAMkin

  • Referenced in 0 articles [sw19002]
  • from the frequently applied software programs ADF, CHARMM, CPMD, CP2K, Gaussian, Q-Chem, and VASP...
  • pyPcazip

  • Referenced in 0 articles [sw20634]
  • most contemporary MD engines such as AMBER, CHARMM, GROMACS and NAMD, and is MPI parallelised...
  • GAUSSIAN

  • Referenced in 185 articles [sw06118]
  • Gaussian is an electronic structure program, used by...