GROMACSIMUM

By Kevin(Feng) Chen1, Ian James Campbell1, Carol Song1

1. Purdue University

GROMACSIMUM is a graphical front-end for Gromacs.

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Version 1.6.4 - published on 21 Jun 2017

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Abstract

GROMACSIMUM is a graphical user interface for popular molecular dynamics package, GROMACS. It is a software package primarily developed for biological MD and offers a huge amount of possible options and settings for tailoring the simulations. Seamlessly integrated with newly developed GUI interfaces, GROMACSIMUM provides comprehensive setup, simulation, analysis and job submission tools. GROMACSIMUM’s combined accuracy and speed make possible long time molecular dynamics simulations. With its highly visual, easy-to-use interface, GROMACSIMUM guides you through each stage of the MD simulation process; in guiding your project workflow, its user friendly environment directs you to a successful outcome. Users inexperienced in MD can work along prepared workflows, while experts may enjoy a significant relief from the tedium of typing and scripting. The current version of the GROMACSIMUM interface features options including: 1. Get the most from your research • A unified interface for all GROMACS simulation tools. • Advanced project management system. • A powerful molecular design and 3D protein visualization tool. • Access your models and data from anywhere in the world. 2. Easy-to-use, instantly interactive • Newly incorporated workflow management system. • A significant relief from tedium of typing and scripting • Easy job submission mechanism. • Dedicated HPC resources. 3. Fully supported by state-of-art simulation technology • Combining leading force fields, accurate effective solvation models. • High-performance ab initio calculations for both gas and solution phase simulations. • Hybrid Quantum Mechanics/Molecular Mechanics. • Free Energy Perturbation and metadynamics simulations. • Support for implicit solvent models. 4. Data analysis and decision making • Plotting, editing, visual data mining and filtering to identify key interactiolns. • Built-in plot and MD trajectory viewer. • Seamless support for Xmgrace, VMD, pymol, rasmol and other 3rd party software packages. For more usage information, see the User Guide. https://diagrid.org/resources/gromacsimum/supportingdocs Questions can be submitted in the GROMACSIMUM tool page. https://diagrid.org/resources/gromacsimum/questions

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Credits

Ian Campbell, Carol Song and Feng (Kevin) Chen

Sponsored by

1. Diagrid.org 2. Information Technology at Purdue

References

1. jSimMacs is a graphical user interface for molecular dynamics simulations with GROMACS. Copyright (C) 2008 Sanjit Roopra (sanjit.roopra@gmail.com) 2. GROMACSIMUM uses the libary Biojava 1.6, Jmol 11.4, jcommon 1.0.12 and jfreechart 1.0.9. The LGPL-License 3.0 can be read in the file lgpl-3.0.txt. The LGPL-License 2.1 can be read in the file lgpl-2.1.txt 3. This product includes software which is published under the Apache License 2.0.GROMACSIMUM uses the libary swingutil, and batik 1.7.The Apache License 2.0 can be read in the file LICENSE-2.0.txt.

Citations

Ian James Campbell, Carol Song, and Feng Chen. “GROMACSIMUM: A Web-based Application for Molecular Dynamics Simulations”, Biophysical Society 58th Annual Meeting, San Francisco, CA, United States, Feb (2014). Carol Song, Rob Campbell, Feng (Kevin) Chen, Steve Clark, Brian Raub, Christopher Thompson. “DiaGrid + HUBzero: Power to the People.”HUBbub 2013, Indianpolis, IN, United States, September, 5-6 (2013).

Cite this work

Researchers should cite this work as follows:

  • Kevin(Feng) Chen; Ian James Campbell; Carol Song (2017), "GROMACSIMUM," https://diagrid.org/resources/gromacsimum.

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