Bio-molecular Simulation

Main page

This is the compilation results of my simulation for completing the "hello world" tutorial using biomolecular modelling software. The link source of the tutorials that are provided.
Do not forget check the Readme in each section for more information and link to the source.

Disclaimer

All of the copyright that been used belongs to the source of the tutorial.

Setup (on Windows 10)

• WSL2 WSL is Windows sub-Linux which we can use a Linux subsystem in the Windows operating system so we can use Linux specific only biomolecular software. for more information on how to install WSL2 on windows go to this link: https://erikbreslmayr.medium.com/gromacs-on-windows10-ac38fa5653e
• GUI on WSL2 up until this text was written the official GUI for WSL2 was not provided by Microsoft. Therefore using another third-party system to connect it via Remote Desktop Connection. This is the link source that I follow the instruction for providing GUI on my WSL2 system : https://davidbombal.com/wsl2-ubuntu-gui/

Molecular Dynamic Simulation

• Gromacs
• NAMD
• Biobb-based gromacs

Molecular Visualization

• Pymol
• VMD

Molecular Docking

• Autodock
• Autodock-vina

cloud based simulation

• Google-Collab Protein-ligand simulation (gromacs)

Muhammad Rady Irawan 23-04-2021