MD on Google Colab

Building/Installing GROMACS 2021 with GPU support on Google Colab

• Build takes around 65 minutes
• Pre-build binary and tutorial is available here→

Useful options

• -nb gpu : to run with GPU
• -noappend : ?
• -cpi CHECKPOINT_FROM_DEFFNAME : ?
• -maxh HOURS_IN_INT : Numbers of hours to execute, terminate yourself before colab terminates it to avoid loss of data or file corruptions

Installing NAMD on Google Colab

Use Python script (can be copied to Colab Notebook Cell) file to execute code to build gromacs on google colab's ubuntu environment with GPU RunTime turned on.

Installing Desmond on Google Colab

• Copy desmond installer to google drive and install desmond on every colab instance start

Plotting Graphs in R and Python

• Python - Python based Utility has been moved to separate repository with executable files
  • Bulk XVG file plotting and value extraction
• R - Directly plot using R