https://github.com/becksteinlab/adkgromacstutorial
Basic tutorial for running and analyzing a Gromacs MD simulation of AdK
Science Score: 23.0%
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Repository
Basic tutorial for running and analyzing a Gromacs MD simulation of AdK
Basic Info
- Host: GitHub
- Owner: Becksteinlab
- License: bsd-3-clause
- Language: Shell
- Default Branch: master
- Homepage: https://AdKGromacsTutorial.readthedocs.org
- Size: 22 MB
Statistics
- Stars: 9
- Watchers: 2
- Forks: 7
- Open Issues: 4
- Releases: 0
Topics
Metadata Files
README.md
AdK Gromacs Tutorial
The full tutorial is available online through Read the Docs.
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 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:
- 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
- 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
Perform energy minimization
Perform position-restrained equilibration
Run production MD in the NPT ensemble
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
Owner
- Name: Becksteinlab
- Login: Becksteinlab
- Kind: organization
- Email: obeckste@asu.edu
- Location: Tempe, AZ
- Website: https://becksteinlab.physics.asu.edu
- Repositories: 56
- Profile: https://github.com/Becksteinlab
Computational Biophysics at Arizona State University
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- orbeckst (4)
- sseyler (2)
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