DL_POLY 4.09.1 – Molecular Dynamics Simulations

DL_POLY 4.09.1

:: DESCRIPTION

DL_POLY is a general purpose classical molecular dynamics (MD) simulation software.

::DEVELOPER

DL_POLY team

:: SCREENSHOTS

DL_POLY

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 DL_POLY

:: MORE INFORMATION

Citation

Philos Trans A Math Phys Eng Sci. 2004 Sep 15;362(1822):1835-52.
DL_POLY_3: the CCP5 national UK code for molecular-dynamics simulations.
Todorov IT1, Smith W.

MDynaMix 5.2.8 – Molecular Dynamics Program

MDynaMix 5.2.8

:: DESCRIPTION

MDynaMix is a general purpose molecular dynamics code for simulations of mixtures of either rigid or flexible molecules, interacting by a force field consisting of Lennard-Jones, electrostatic, covalent bonds, angles and torsion angles potentials as well as of some optional terms, in a periodic rectangular, hexagonal or truncated octahedron cell. Rigid bonds are constrained by the SHAKE algorithm. In case of flexible molecular models the double time step algorithm is used. Algorithms for NVE, NVT and NPT statistical ensembles are implemented, as well as Ewald sum for treatment of the electrostatic interactions. Treatment of quantum correction to the atomic motion can be done within the Path Integral Molecular Dynamics approach. Possibility for free energy computations by the expanded ensemble method is included.

::DEVELOPER

Lyubartsev, Alexander

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  MDynaMix

:: MORE INFORMATION

Citation

A.P.Lyubartsev, A.Laaksonen,
MDynaMix – A scalable portable parallel MD simulation package for arbitrary molecular mixtures”
Computer Physics Communications, 128, 565-589 (2000).

MM-ISMSA – Scoring Function for Protein-Protein and Protein-Ligand Docking and Molecular Dynamics

MM-ISMSA

:: DESCRIPTION

MM-ISMSA is an ultrafast and accurate scoring function for protein-protein and protein-ligand docking

::DEVELOPER

Unidad de Bioinformatica CBMSO

:: SCREENSHOTS

MM-ISMSA

:: REQUIREMENTS

  • Windows / Linux
  • Python
  • PyMOL

:: DOWNLOAD

  MM-ISMSA

:: MORE INFORMATION

Citation

Javier Klett, Alfonso Núñez-Salgado, Helena G. Dos Santos, Álvaro Cortés-Cabrera, Almudena Perona, Rubén Gil-Redondo, David Abia, Federico Gago, and Antonio Morreale
MM-ISMSA: an ultra-fast and accurate scoring function for protein-protein docking.
J Chem Theory Comput. 2012 Sep 11;8(9):3395-3408

NAMD 2.11b1 – Molecular Dynamics Program

NAMD 2.11b1

:: DESCRIPTION

NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. Simulation preparation and analysis is integrated into the visualization package VMD.

::DEVELOPER

Theoretical and Computational Biophysics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX

:: DOWNLOAD

 NAMD

:: MORE INFORMATION

Citation:

Scalable molecular dynamics with NAMD.
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L, Schulten K.
J Comput Chem. 2005 Dec;26(16):1781-802.

GOdMD – Conformational Transitions with discrete Molecular Dynamics

GOdMD

:: DESCRIPTION

GOdMD is a new method for determining pathways for conformational transitions in macromolecules based on the use of discrete molecular dynamics and biasing techniques based on a combination of essential dynamics and Maxwell-Demon sampling techniques.

::DEVELOPER

Molecular Modeling and Bioinformatics Unit , IRB Barcelona

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Aug 15;29(16):1980-6. doi: 10.1093/bioinformatics/btt324. Epub 2013 Jun 5.
Exploration of conformational transition pathways from coarse-grained simulations.
Sfriso P1, Hospital A, Emperador A, Orozco M.

do_x3dna 20141212 – Analyze Fluctuations in DNA or RNA Structures in Molecular Dynamics Trajectories

do_x3dna 20141212

:: DESCRIPTION

The do_x3dna package has been developed to analyze the structural fluctuations of DNA or RNA during molecular dynamics simulations.

::DEVELOPER

Rajendra Kumar

:: SCREENSHOTS

N/a

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  • 3DNA

:: DOWNLOAD

 do_x3dna

:: MORE INFORMATION

Citation

do_x3dna: A tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations.
Kumar R, Grubmüller H.
Bioinformatics. 2015 Apr 2. pii: btv190.

Ayla 0.1.1 – Visualization tool for researchers in Biochemistry, Molecular Dynamics, and Protein Folding

Ayla 0.1.1

:: DESCRIPTION

Ayla is a free, open source visualization tool for researchers in biochemistry, molecular dynamics, and protein folding.

::DEVELOPER

Ayla team

:: SCREENSHOTS

Ayla

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • Java

:: DOWNLOAD

  Ayla

:: MORE INFORMATION

Citation:

A collaborative visual analytics suite for protein folding research.
Harvey W, Park IH, Rübel O, Pascucci V, Bremer PT, Li C, Wang Y.
J Mol Graph Model. 2014 Sep;53:59-71. doi: 10.1016/j.jmgm.2014.06.0

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

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

MDWeb / MDMoby – Web-based Platform for Molecular Dynamics Simulations

MDWeb / MDMoby

:: DESCRIPTION

MDWeb is a personal workspace providing standard protocols to prepare structures, run standard molecular dynamics simulations and to analyze trajectories. MDWeb and MDMoby constitute a web-based platform to help access to molecular dynamics (MD) in the standard and high-throughput regime. The platform provides tools to prepare systems from PDB structures mimicking the procedures followed by human experts. It provides inputs and can send simulations for three of the most popular MD packages (Amber, NAMD and Gromacs). Tools for analysis of trajectories, either provided by the user or retrieved from our MoDEL database are also incorporated.

::DEVELOPER

the Molecular Recognition & Bioinformatics Group.

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.
Hospital A, Andrio P, Fenollosa C, Cicin-Sain D, Orozco M, Gelpí JL.
Bioinformatics. 2012 May 1;28(9):1278-9. Epub 2012 Mar 21.