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Molecular Dynamics Simulation Pdf software
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Molecular Dynamics Simulation Pdf

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Released: November 23, 2012  |  Added: November 23, 2012 | Visits: 235

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: November 12, 2013 | Visits: 280

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: November 13, 2013 | Visits: 275

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: 223

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: January 17, 2010 | Visits: 882

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: December 12, 2012  |  Added: December 12, 2012 | Visits: 276

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

Added: September 01, 2013 | Visits: 295

Kirchhoff Vortex Contour Dynamics Simulation A Kirchhoff elliptic vortex is a 2D elliptical region (or d-deDUpatchd-deDt) of uniform vorticity embedded in an inviscid, incompressible and irrotational fluid. G. Kirchhoff showed that these are exact solutions to the nonlinear Euler equations in 1876.Subsequently, A. E. H. Love analyzed the...


Platforms: Matlab

License: Freeware Size: 829.44 KB Download (23): Kirchhoff Vortex Contour Dynamics Simulation 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: 289

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 06, 2012  |  Added: August 06, 2012 | Visits: 341

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

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: 218

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: 216

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

Added: July 25, 2013 | Visits: 123

Pressure on water Molecular Workbench simulation of a polypeptide crystal. Use the slider in the top right to increase the temperature of the system until the polypeptides lose their original form. Cool the system. Why don't the polypeptides regenerate their original forms?


Platforms: Mac

License: Shareware Cost: $0.00 USD Size: 1.02 KB Download (18): Pressure on water Download

Added: September 22, 2010 | Visits: 625

ToBiX ToBiX is a Morphix-based Linux live CD containing a range of specialist applications for bioinformatics. With this distrubution you just boot from the CD and you have a fully functional LINUX OS distribution with open source applications. Besides using some RAM, ToBiX doesnt touch the host...


Platforms: *nix

License: Freeware Size: 457.2 MB Download (73): ToBiX 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

Released: November 13, 2012  |  Added: November 13, 2012 | Visits: 258

Sphinx SD Tools The Sphinx project is dedicated to create common accessible environment for system dynamics simulation. This software is developed on Java 6 platform and use Java Swing GUI.


Platforms: Windows, Mac, Linux

License: Freeware Size: 5.64 MB Download (27): Sphinx SD Tools Download

Added: November 09, 2013 | Visits: 209

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: 124

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

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