https://github.com/becksteinlab/adkgromacstutorial

Basic tutorial for running and analyzing a Gromacs MD simulation of AdK
https://github.com/becksteinlab/adkgromacstutorial

gromacs molecular-dynamics-simulation tutorial

Last synced: 9 months ago
JSON representation

Basic tutorial for running and analyzing a Gromacs MD simulation of AdK

• Host: GitHub
• URL: https://github.com/becksteinlab/adkgromacstutorial
• Owner: Becksteinlab
• License: bsd-3-clause
• Created: 2016-08-18T00:44:09.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2018-07-03T15:03:07.000Z (over 7 years ago)
• Last Synced: 2025-04-02T06:43:08.497Z (10 months ago)
• Topics: gromacs, molecular-dynamics-simulation, tutorial
• Language: Shell
• Homepage: https://AdKGromacsTutorial.readthedocs.org
• Size: 22 MB
• Stars: 9
• Watchers: 2
• Forks: 7
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

          
AdK Gromacs Tutorial

====================

[![docs](https://readthedocs.org/projects/adkgromacstutorial/badge/)](https://readthedocs.org/projects/adkgromacstutorial)



The full tutorial is available online through

[Read the Docs](http://adkgromacstutorial.readthedocs.io).

Objective

---------

Perform an all-atom molecular dynamics (MD) simulation—using the [Gromacs]

MD package—of the apo enzyme adenylate kinase (AdK) in its open conformation in

a physiologically realistic environment, and carry out a basic analysis of its

structural properties in equilibrium.

Tutorial files

--------------

All of the necessary tutorial files can obtained by cloning the repository

```bash

  git clone https://github.com/Becksteinlab/AdKGromacsTutorial.git

```

Workflow overview

-----------------

For this tutorial we'll use [Gromacs] (version 5.1.3) to set up the system, run

the simulation, and perform analysis. An initial structure is provided, which

can be found in the :file:`tutorial/templates` directory, as well as the MDP

files that are necessary for input to Gromacs. The overall workflow consists of

the following steps:

1. Download tutorial files and set up working directories

   - Obtain structure 4AKE from [PDB]

   - Generate a stripped PDB file containing only chain A and no crystal waters

2. Solvate the protein system

   - Generate topology using default protonation states

   - Solvate in water in simulation cell (rhombic dodecahedron)

   - Ionize system with NaCl to neutralize and obtain physiological concentration

3. Perform energy minimization

4. Perform position-restrained equilibration

5. Run production MD in the NPT ensemble

6. Visualize the trajectory

   - Center the protein in a box with primitive unitcell representation (periodic boundary conditions)

   - RMS-fit the protein in each snapshot to the first snapshot

[Gromacs]: http://www.gromacs.org

[PDB]: http://www.rcsb.org/pdb/home/home.do