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Molecular Simmulation software
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Molecular Simmulation

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Added: August 14, 2013 | Visits: 265

Hidden Markov Models for Molecular Motors Hidden Markov models are used to describe the "stepping" behavior of molecular motors, as measured by single-molecule fluorescence techniques. Our HMM implementation is more versatile than the one described by Milescu, et al. Biophys. J. 91:3135-3150 and can be used as a "blind" step detector or...



Platforms: Matlab

License: Freeware Size: 829.44 KB Download (19): Hidden Markov Models for Molecular Motors Download

Added: August 12, 2013 | Visits: 274

ORMA (Oligonucleotide Retrieving for Molecular Applications) ORMA (Oligonucleotide Retrieving for Molecular Applications) is a series of integrated scripts in Matlab, which performs an accurate search of all the positions able to specifically discriminate one species among homologous ones. ORMA also performs an accurate selection of high-quality...





Platforms: Matlab

License: Freeware Size: 286.72 KB Download (18): ORMA (Oligonucleotide Retrieving for Molecular Applications) Download

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

Released: May 26, 2017  |  Added: June 04, 2017 | Visits: 1.986

CHEMIX School CHEMIX School is an educational tool for learning chemistry. It is geared toward college-level chemistry, but is also appropriate for high-school students, chemists, and teachers. It is equipped with a periodic table containing history, 19 physical properties + number of stable isotopes,...


Platforms: Windows, Windows 8, Windows 7, Windows Server

License: Shareware Cost: $19.00 USD Size: 1.45 MB Download (226): CHEMIX School Download

Added: August 12, 2008 | Visits: 1.673

Molecular Weight Calculator for Pocket PC Molecular Weight Calculator is an easy to use program to calculate the mass of a molecular formula and composition of each atom. Allows entry of chemical formulas in commonly-used syntax both empirical and molecuar formula.This innovative program provides a fast and easy-to-use tool. This is an...


Platforms: Pocket PC 2002

License: Commercial Cost: $5.00 USD Size: 453 KB Download (220): Molecular Weight Calculator for Pocket PC Download

Added: August 13, 2010 | Visits: 984

Avogadro Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. This project offers a flexible rendering engine and a powerful plugin architecture. The main concept behind Avogadro...


Platforms: *nix

License: Freeware Size: 256 KB Download (138): Avogadro Download

Added: July 22, 2010 | Visits: 851

Bio::MCPrimers Bio::MCPrimers is a Perl module to create molecular cloning PCR primer pairs for a given gene so that the gene can be directionally inserted into a vector. Solver is generic, restriction enzymes and their order in the vector are specified in the caller. XPORT SUBROUTINES sub find_mc_primers...


Platforms: *nix

License: Freeware Size: 174.08 KB Download (81): Bio::MCPrimers 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: June 21, 2012  |  Added: June 21, 2012 | Visits: 293

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: October 24, 2012  |  Added: October 24, 2012 | Visits: 259

BALLView BALLView is our standalone molecular modeling and visualization application. Furthermore it is also a framework for developing molecular visualization functionality. It is available free of charge under the GPL for Linux, Windows and MacOS. It provides fast OpenGL-based visualization of...


Platforms: Windows

License: Freeware Size: 38 MB Download (50): BALLView Download

Released: September 05, 2012  |  Added: September 05, 2012 | Visits: 251

PyMOL PyMOL is a user-sponsored molecular visualization system on an open-source foundation. Please support development of this open, effective, and affordable software by purchasing an incentive copy, which is pre-built and comes with maintenance and support. PyMOL can interpret over 30 different...


Platforms: Windows, Mac, Linux

License: Freeware Size: 9.1 MB Download (49): PyMOL 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

Released: September 06, 2012  |  Added: September 06, 2012 | Visits: 351

Facio Facio is an OpenGL-based 3D-graphics program for molecular modeling and visualization of quantum chemical calculations (GAMESS and Gaussian). SSH / SFTP client is also implemented. Through SSH / SFTP connection, Gaussian job can be submitted to batch job system on the remote server and...


Platforms: Windows

License: Freeware Size: 15.7 MB Download (51): Facio Download

Released: October 02, 2012  |  Added: October 02, 2012 | Visits: 327

Geneious Basic Geneious is a useful, unique and easy-to-use software system which has been designed to greatly speed up and simplify the research in molecular biology and biochemistry. Geneious is a cross-platform research engine for the retrieval, organization and analysis of biomolecular data that allows...


Platforms: Windows

License: Freeware Size: 39.6 MB Download (63): Geneious Basic Download

Released: November 04, 2012  |  Added: November 04, 2012 | Visits: 331

MOPlot MOPlot is a handy visualization application specially designed for fast molecular orbitals plotting from the outputs of the Gaussian 03/98/94, Molcas, Gamess/US quantum chemical calculation packages. This Molecular Orbital Plotting Program will prove to be easy-to-use and very efficient. MOPlot...


Platforms: Windows, XP

License: Freeware Download (62): MOPlot Download

Released: November 24, 2012  |  Added: November 24, 2012 | Visits: 330

Geneious Basic x64 Geneious is a useful, unique and easy-to-use software system which has been designed to greatly speed up and simplify the research in molecular biology and biochemistry. Geneious is a cross-platform research engine for the retrieval, organization and analysis of biomolecular data that allows...


Platforms: Windows

License: Freeware Size: 39.6 MB Download (62): Geneious Basic x64 Download

Released: November 07, 2012  |  Added: November 07, 2012 | Visits: 214

Open3DGRID x64 Open3DGRID is an application designed for high-throughput generation of molecular interaction fields or MIFs. Open3DGRID can generate steric potential, electron density and MM / QM electrostatic potential fields; furthermore, it can import GRIDKONT binary files produced by GRID and CoMFA / CoMSIA...


Platforms: Windows

License: Freeware Download (53): Open3DGRID x64 Download

Released: August 17, 2012  |  Added: August 17, 2012 | Visits: 229

Open3DGRID for Linux Open3DGRID is an application designed for high-throughput generation of molecular interaction fields or MIFs. Open3DGRID can generate steric potential, electron density and MM / QM electrostatic potential fields; furthermore, it can import GRIDKONT binary files produced by GRID and CoMFA / CoMSIA...


Platforms: Linux

License: Freeware Download (45): Open3DGRID for Linux Download

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