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Molecular Dynamics Newsgroup software
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Molecular Dynamics Newsgroup

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Added: November 13, 2013 | Visits: 277

Molecular Dynamics Model The EJS Molecular Dynamics model is constructed using the Lennard-Jones potential truncated at a distance of 3 molecular diameters. The motion of the molecules is governed by Newton's laws, approximated using the Verlet algorithm with the indicated time step. For sufficiently small time steps dt,...



Platforms: Mac

License: Freeware Size: 1.3 MB Download (17): Molecular Dynamics Model Download

Added: July 24, 2013 | Visits: 224

Molecular Dynamics Demonstration Model The EJS Molecular Dynamics Demonstration model is constructed using the Lennard-Jones potential truncated at a distance of 3 molecular diameters. The motion of the molecules is governed by Newton's laws, approximated using the Verlet algorithm with the indicated Time step. For sufficiently small...





Platforms: Mac

License: Freeware Size: 1.3 MB Download (16): Molecular Dynamics Demonstration Model Download

Added: November 12, 2013 | Visits: 283

Molecular Dynamics Adiabatic Piston Model The Molecular Dynamics Adiabatic Piston model shows two gas samples within a horizontal cylinder that is divided by an insulated piston that moves without friction. It is a supplemental simulation for an article by Eric Gislason "A close examination of the motion of an adiabatic piston" in the...


Platforms: Mac

License: Freeware Size: 1.12 MB Download (17): Molecular Dynamics Adiabatic Piston Model Download

Added: January 17, 2010 | Visits: 883

LAMMPS LAMMPS project is a Molecular Dynamics Simulator. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grain systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the mesoscale...


Platforms: *nix

License: Freeware Download (109): LAMMPS Download

Released: November 23, 2012  |  Added: November 23, 2012 | Visits: 236

Polarizable Fluids Molecular Dynamics PFMD performs a Molecular Dynamics simulation of some polarizable fluids at the liquid state by means of a dissociable potential. Supported molecules are H2O (water) and MX3, where M is a metal among Al, Fe, or Ga and X is a halogen among Cl, Br, or I.


Platforms: Windows, Mac, Linux

License: Freeware Size: 347.03 KB Download (29): Polarizable Fluids Molecular Dynamics Download

Added: July 01, 2013 | Visits: 202

Sander 8 Job Controls Sander is the AMBER module which carries out energy minimization, molecular dynamics, and NMR refinements. The acronym stands for Simulated Annealing with NMR-Derived Energy Restraints, but this module is used for a variety of simulations that have nothing to do with NMR refinement. Sander uses...


Platforms: Mac

License: Shareware Cost: $0.00 USD Size: 143.36 KB Download (17): Sander 8 Job Controls Download

Released: June 21, 2012  |  Added: June 21, 2012 | Visits: 292

Open3DALIGN x64 Open3DALIGN is an open-source software aimed at unsupervised molecular alignment. Open3DALIGN is a command-line tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or piped through standard input. If PyMOL is...


Platforms: Windows

License: Freeware Size: 5.2 MB Download (46): Open3DALIGN x64 Download

Released: August 04, 2012  |  Added: August 04, 2012 | Visits: 229

Open3DALIGN for Mac OS X Open3DALIGN is an open-source software aimed at unsupervised molecular alignment. Open3DALIGN is a command-line tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or piped through standard input. If PyMOL is...


Platforms: Mac

License: Freeware Size: 3.6 MB Download (44): Open3DALIGN for Mac OS X Download

Released: June 03, 2012  |  Added: June 03, 2012 | Visits: 220

Open3DALIGN Open3DALIGN is an open-source software aimed at unsupervised molecular alignment. Open3DALIGN is a command-line tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or piped through standard input. If PyMOL is...


Platforms: Windows

License: Freeware Size: 4.1 MB Download (42): Open3DALIGN Download

Released: August 07, 2012  |  Added: August 07, 2012 | Visits: 217

Open3DALIGN for Linux Open3DALIGN is an open-source software aimed at unsupervised molecular alignment. Open3DALIGN is a command-line tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or piped through standard input. If PyMOL is...


Platforms: Linux

License: Freeware Size: 3.3 MB Download (41): Open3DALIGN for Linux Download

Released: December 12, 2012  |  Added: December 12, 2012 | Visits: 277

Gromacs for Mac OS X and Linux GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded...


Platforms: Mac, Linux

License: Freeware Size: 9.92 MB Download (101): Gromacs for Mac OS X and Linux Download

Released: September 01, 2012  |  Added: September 01, 2012 | Visits: 187

jSim for Gromacs jSim for Gromacs is a Graphical User Interface for the Molecular Dynamics Package Gromacs. It has a project style interface to organize your md simulations. It is also possible to start md simulations on remote computers with ssh.


Platforms: Windows, Mac, Linux

License: Freeware Size: 7.19 MB Download (27): jSim for Gromacs Download

Released: December 14, 2012  |  Added: December 14, 2012 | Visits: 219

MolecuLab - Modelling Interface This project aims to develop a cross platform environment for utilisation of various open source and freely available molecular dynamics and bioinformatics tools. Some extra features are included such as protein hydrophobicity and hydrophilicity plots.


Platforms: Windows, Mac, Linux

License: Freeware Size: 5.17 KB Download (28): MolecuLab - Modelling Interface Download

Added: November 09, 2013 | Visits: 212

MDAnalysis MDAnalysis is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, NAMD, LAMMPS, or Amber. It allows one to read molecular dynamics trajectories and access the atomic coordinates through numpy arrays. This provides a flexible and relatively...


Platforms: Mac

License: Freeware Size: 19.01 MB Download (16): MDAnalysis Download

Added: November 07, 2013 | Visits: 125

MDAnalysisTests MDAnalysis is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, NAMD, LAMMPS, or Amber. It allows one to read molecular dynamics trajectories and access the atomic coordinates through numpy arrays. This provides a flexible and relatively...


Platforms: *nix

License: Shareware Cost: $0.00 USD Size: 18.25 MB Download (16): MDAnalysisTests Download

Added: September 06, 2013 | Visits: 181

Ascalaph Graphics for Linux Ascalaph Graphics is a program for molecular graphics and dynamics, as well as a graphical shell to package of molecular dynamics MDynaMix. Features: Molecular graphics Multiple windows Two cameras per model CPK, Wire frame, Stick, Ball and Stick and CPK Wire frame styles Molecular...


Platforms: *nix

License: Freeware Size: 16.15 MB Download (18): Ascalaph Graphics for Linux Download

Released: August 06, 2012  |  Added: August 06, 2012 | Visits: 342

Ascalaph Designer The Ascalaph Designer application was developed for molecular models and simulations. Using this application you can simulate, molecular graphics, optimization, molecular dynamics, quantum chemistry. Features: Molecular graphics Multiple windows Two cameras per model CPK, Wire frame,...


Platforms: Windows

License: Freeware Size: 72 MB Download (46): Ascalaph Designer Download

Added: July 18, 2013 | Visits: 270

MDDriver MDDriver is a library allowing a user to easily couple molecular visualisation tools with simulation code through a network. It allows to carry out interactive molecular dynamics, visualize simulation results and drive a simulation in interactive time.


Platforms: *nix

License: Freeware Size: 104.88 MB Download (27): MDDriver Download

Added: May 10, 2013 | Visits: 212

gdpc gdpc is a program for visualising molecular dynamic simulations. It is a very versatile program and could easily be used for any other purposes.gdpc reads xyz input and custom formats and can write out pictures of the frames. Requirements: - gtk+


Platforms: *nix, C/C++, BSD

License: Freeware Download (28): gdpc Download

Added: June 22, 2013 | Visits: 260

Nanodesigner Nanodesigner is a software platform for research on molecular nanotechnology. It has a plug-in architecture and will include tools for molecular visualization & modelling, design of complex new molecules, molecular dynamics,...


Platforms: *nix

License: Freeware Size: 2.16 MB Download (21): Nanodesigner Download

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