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1. Text link: GROMACS - Gromacs

Domain: www.gromacs.org

Link: http://www.gromacs.org/

Description: GROMACS survey. 2020 GROMACS user survey is now live. The survey will help the GROMACS developers to prioritise future GROMACS developments. We would like input from researchers who perform any and all forms of molecular dynamics and whose experience using GROMACS ranges from zero experience to expert active users.

2. Text link: GROMACS - Wikipedia

Domain: en.wikipedia.org

Link: https://en.wikipedia.org/wiki/GROMACS

Description: GROMACS is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids.It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers worldwide. GROMACS is one of the fastest and most popular software packages available, and can run on central ...

3. Text link: GROMACS Tutorials

Domain: www.mdtutorials.com

Link: http://www.mdtutorials.com/gmx/

Description: GROMACS is free, open-source software, and has consistently been one of the fastest (if not the fastest) molecular dynamics codes available. There are currently seven tutorials available: Lysozyme in Water: The intent of this tutorial is to give new users a basic introduction into the tools used to prepare, run, and perform simple analysis on a "typical" system with GROMACS.

4. Text link: GROMACS - an overview | ScienceDirect Topics

Domain: www.sciencedirect.com

Link: https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/gromacs

Description: GROMACS freeware was used to perform the Molecular Dynamic Simulations for the native and mutant MSH2-MSH6 complexes (Abraham et al., 2015). CHARMM36 all-atom lipid force field (with CMAP) was used to generate the topologies for the native and mutant complexes. The complexes were solvated in a cubical box with SPC (Single Point Charge) water ...

5. Text link: Welcome to the GROMACS documentation!

Domain: manual.gromacs.org

Link: https://manual.gromacs.org/documentation/

Description: Two versions of GROMACS are under active maintenance, the 2019 series and the 2018 series. In the latter, only highly conservative fixes will be made, and only to address issues that affect scientific correctness. Naturally, some of those releases will be made after the year 2018 ends, but we keep 2018 in the name so users understand how up to date ...

6. Text link: Gromacs download | SourceForge.net

Domain: sourceforge.net

Link: https://sourceforge.net/projects/gromacs/

Description: Download Gromacs for free. Gromacs for Windows. 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.

7. Text link: GROMACS Tutorial

Domain: www.mdtutorials.com

Link: http://www.mdtutorials.com/gmx/lysozyme/index.html

Description: GROMACS Tutorial Lysozyme in Water. Justin A. Lemkul, Ph.D. Virginia Tech Department of Biochemistry. This example will guide a new user through the process of setting up a simulation system containing a protein (lysozyme) in a box of water, with ions. Each step will contain an explanation of input and output, using typical settings for general ...

8. Text link: Molecular dynamics parameters (.mdp options) — GROMACS ...

Domain: manual.gromacs.org

Link: https://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html

Description: In GROMACS, normal reaction-field electrostatics with cutoff-scheme = cutoff-scheme=group leads to bad energy conservation. coulombtype=Reaction-Field-zero solves this by making the potential zero beyond the cut-off. It can only be used with an infinite dielectric constant (epsilon-rf =0), because only for that value the force vanishes at the cut-off.

9. Text link: Installing Gromacs on Ubuntu for MD Simulation ...

Domain: bioinformaticsreview.com

Link: https://bioinformaticsreview.com/20151126/how-to-install-gromacs-5-x-x-on-linux-ubuntu-14-04-lts/

Description: In bioinformatics, GROMACS is one of the most popular Molecular Dynamics simulation software with loads of features built-in. Installing GROMACS Version 5.x.x+ can be a tedious and cumbersome process on Ubuntu, especially if you are just starting out. For beginners, installing and getting GROMACS to work is more challenging due to unfamiliarity with Linux commands

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