Name: AdKGromacsTutorial
Owner: Becksteinlab
Description: Basic tutorial for running and analyzing a Gromacs MD simulation of AdK
Created: 2016-08-18 00:44:09.0
Updated: 2017-06-01 21:27:33.0
Pushed: 2017-03-30 21:35:31.0
Homepage: https://AdKGromacsTutorial.readthedocs.org
Size: 23050
Language: Shell
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The full tutorial is available online through Read the Docs.
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.
All of the necessary tutorial files can obtained by cloning the repository
t clone https://github.com/Becksteinlab/AdKGromacsTutorial.git
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:
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