gmx-helper README

gmx-helper extension is a vscode extension to help editing gromacs-related files, e.g., top, itp, mdp, etc..

The purpose I write these code is to make Molecular Dynamics (MD) Simulation easier to perform, by changing the view of the sections in the files above into different colors, so that you can pay more attention on the parameters to edit; also, it will be more convinent to edit mdp and top file ny using templates.

Documentation: https://zhuanlan.zhihu.com/p/395063324 (In Chinese)

Features

Hightlights

The gmx-helper extension helps changing the view of a set of gromacs-related files. Below shows the new views of those files after installing gmx-helper extension.

• The coordinates of gro and ndx files colored into blue.

• The contents in square brackets of itp and top files colored into green.

• The frequently-used keywords of mdp files colored into purple.

• The rtp files are also included because sometimes we need to write topology of self-defined residues so that we could use pdb2gmx to build the protein topology including non-protein residues, and during this, the rtp file is necessary to provide parameters for gromacs to use in various forcefields (amber, gromos, etc.). See this article for details Methods of making self-defined residues in GROMOS forcefield (in Chinese).

Quick Editing mdp

Helps editing .mdp files by adding snippets as listed below:

• mdp-preprocessing
• mdp-run-control
• mdp-energy-minimization
• mdp-output-control
• mdp-neighbor-searching
• mdp-coulomb-vdW
• mdp-temperature-coupling
• mdp-pressure-coupling
• mdp-simulated-annealing
• mdp-velocity-generation
• mdp-bonds
• mdp-freeze
• mdp-miscellaneous
• lazy-mdp-em
• lazy-mdp-md-nopbc
• lazy-mdp-md-heat
• lazy-mdp-md-npt
• lazy-mdp-md-protein
• lazy-mdp-pr-protein
• lazy-mdp-md-protein-lig
• lazy-mdp-pr-protein-lig

Quick generating top

Helps generating basic structure of topology file (usually named topol.top by pdb2gmx) by typing lazy-topol, and also gives typical topology section sequence at the head of .top file.

Release Notes

1.4.0

Added annealing snippets to .mdp files of protein system.

1.3.0

Added snippets to generate .top file.

1.2.0

Added more precise snippets to generate .mdp files by parts.

1.1.0

Added snippets for writing .mdp files.

1.0.0

Initial release of gmx-helper.

Enjoy!