GROMACS-A Molecular Dynamic Approach

LINUX SYSTEM INSTRUCTION ALONG WITH GROMACS INSTALLATION:

1. If you have newly downloaded the linux system then firstly update it using sudo apt update.(This will download and update all the required packages.)

Open a terminal on linux and type this command.

2. Now to download gromacs in the same terminal type sudo apt install gromacs. ( This will download gromacs in your system)

IMPORTAT POINTS
:
1. You can take the help of online gromacs tutorial for lysozyme in water to perform protein molecular dynamics simulation. (you can access it by typing gromacs tutorial on google and once you open it click on lysozyme in water)

2. DO NOT turn of your system when a step is running in the terminal.

3. Steps from minim.mdp creation will take time to run. Hence, keep the power supply on continously and dont stop the process.

4. When you choose the protein of your interest then wherever it is in steps as 1aki change to the name of your protein that you have downloaded.

5. Generate graphs only after completion of MD run.