Tag: GROMACS

Gromita 4.6 – GUI for GROMACS

Gromita 4.6

:: DESCRIPTION

Gromita is a Graphical User Interface (GUI) for GROMACS (v.3 and 4). It is writen in perl making extensive use of perl/tk achieving portability in a wide variety of operating systems and architectures. Gromita provides friendly to use buttons in a windows-based environment while maintaining a terminal mode for the experienced user.

::DEVELOPER

Gromita Team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 Gromita

:: MORE INFORMATION

Citation

Sellis D, Vlachakis D, Vlassi M. (2009)
Gromita: A Fully Integrated Graphical User Interface to Gromacs 4.
Bioinform Biol Insights 2009:3 99-102

pmx – Python Library and Tools for Computational and Structural Biophysics

pmx

:: DESCRIPTION

pmx (formerly pymacs) has started as a small bunch of classes to read structure files such as pdb or gro and trajectory data in gromacs xtc format. Over the years it has been extended towards a versatile (bio-) molecular structure manipulation package with some additional functionalities, e.g. gromacs file parsers and scripts for setup and analysis of free energy calculations.

::DEVELOPER

Daniel Seeliger

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

pmx

:: MORE INFORMATION

Citation

Biophys J. 2010 May 19;98(10):2309-16. doi: 10.1016/j.bpj.2010.01.051.
Protein thermostability calculations using alchemical free energy simulations.
Seeliger D1, de Groot BL.

Gro2mat – A package to efficiently read Gromacs output in Matlab

Gro2mat

:: DESCRIPTION

gro2mat is a package that allows fast and easy access to Gromacs output files from Matlab.

::DEVELOPER

Oxford Protein Informatics Group (OPIG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • MatLab

:: DOWNLOAD

 Gro2mat

:: MORE INFORMATION

Citation

J Comput Chem. 2014 Jul 30;35(20):1528-31. doi: 10.1002/jcc.23650. Epub 2014 Jun 12.
Gro2mat: a package to efficiently read gromacs output in MATLAB.
Dien H1, Deane CM, Knapp B.

GROMACS 2019.4 – Molecular Simulation

GROMACS 2019.4

:: DESCRIPTION

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 interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

::DEVELOPER

GROMACS Team 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 GROMACS

:: MORE INFORMATION

Citation

Hess, et al. (2008)
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
J. Chem. Theory Comput. 4: 435-447.

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.
Pronk S, Páll S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, Shirts MR, Smith JC, Kasson PM, van der Spoel D, Hess B, Lindahl E.
Bioinformatics (2013) 29 (7): 845-854.

jSim for Gromacs 0.63b – Graphical User Interface for Gromacs

jSim for Gromacs 0.63b

:: DESCRIPTION

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.

::DEVELOPER

Bob Morane

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 jSim for Gromacs

:: MORE INFORMATION