Tag: Simulations

RedMD 2.3 – Perform Molecular Dynamics Simulations for Coarse-grained Models

RedMD 2.3

:: DESCRIPTION

RedMD (Reduced Molecular Dynamics) is a an open source software to perform molecular dynamics simulations for coarse-grained models of proteins, nucleic acids and their complexes. Simulations can be carried out in the microcanonical ensemble, with Berendsen and Langevin thermostats, as well as with Brownian dynamics.

::DEVELOPER

Biomolecular Machines Laboratory 

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RedMD

:: MORE INFORMATION

Citation

Adam Gorecki, Marcin Szypowski, Maciej Dlugosz, Joanna Trylska,
RedMD – reduced molecular dynamics package,
J. Comput. Chem., 30:2364-2373, 2009

Wordom 0.22 rc3 – Analysis of Molecular Dynamics Simulations

Wordom 0.22 rc3

:: DESCRIPTION

Wordom is a (simple) command line utility conceived to spare the user some time in manipulating and converting dcd, xtc, pdb, crd and xyz files. Wordom is also a versatile program for a broad range of molecular structure and dynamics analysis.

::DEVELOPER

the Fanelli Lab at the University of Modena and Reggio Emilia (IT)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Wordom

:: MORE INFORMATION

Citation

M. Seeber, A. Felline, F. Raimondi, S. Muff, Ran Friedman, F. Rao, A. Caflisch and F. Fanelli;
Wordom: a user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces;
J. Comp. Chem., 2011, 6(32):1183-1194; doi:10.1002/jcc.21688

NEURON 7.7.2 – Simulations of Neurons and Networks of Neurons

NEURON 7.7.2

:: DESCRIPTION

NEURON is a simulation environment for developing and exercising models of neurons and networks of neurons. It is particularly well-suited to problems where cable properties of cells play an important role, possibly including extracellular potential close to the membrane), and where cell membrane properties are complex, involving many ion-specific channels, ion accumulation, and second messengers.

::DEVELOPER

NEURON team

:: SCREENSHOTS

NEURON1

:: REQUIREMENTS

  • Linux /Mac OsX / Windows

:: DOWNLOAD

 NEURON

:: MORE INFORMATION

Citation:

NEURON: a tool for neuroscientists.
Hines ML, Carnevale NT.
Neuroscientist. 2001 Apr;7(2):123-35. Review.