HPC/Exascale Centre of Excellence in Personalised Medicine

Lysozyme in Water application

This repository contains the Lysozyme in Water sample application using a set of Building Blocks (BB) that internally use gromacs within the HPC/Exascale Centre of Excellence in Personalised Medicine (PerMedCoE) project.

This example guides users through the process of setting up a simulation system containing a set of proteins (lysozymes) in boxes of water, with ions. Each step contain an explanation of input and output, using typical settings for general use.

Extracted from: http://www.mdtutorials.com/gmx/lysozyme/index.html

Originally done by: Justin A. Lemkul, Ph.D.

From: Virginia Tech Department of Biochemistry

NOTE: This example reaches up to stage 4 (energy minimization).

Table of Contents

• HPC/Exascale Centre of Excellence in Personalised Medicine
  • Lysozyme in Water application
  • Table of Contents
  • Repository contents
  • Requirements
  • Usage
    • 1st - Install permedcoe package
    • 2th - Download the Lysozyme in water sources
    • 3th - Create the Singularity container
    • 4th - Install the gromacs_BBs Building Blocks
    • 5th - Execute the lysozyme_in_water application
      • 5.1 Bare: Sequential implementation as a bash script using the building blocks directly.
      • 5.2 SnakeMake: Parallelized with SnakeMake.
      • 5.3 PyCOMPSs: Parallelized with PyCOMPSs.
  • License
  • Contact

Repository contents

• PerMedCoE: PerMedCoE base package.
• gromacs_BBs: Set of building blocks using gromacs.
• application: Lysozyme in water application using the gromacs_BBs

Requirements

• Python >= 3.6
• Singularity
• PyCOMPSs
• (Optional: For results visualization) Grace

Usage

1^st - Install permedcoe package

python3 -m pip install permecoe

2^th - Download the Lysozyme in water sources

git clone https://github.com/PerMedCoE/Lysozyme_in_water.git

3^th - Create the Singularity container

cd Lysozyme_in_water/gromacs_BBs/image
./build.sh
cd ..

4^th - Install the gromacs_BBs Building Blocks

./install_BBs.sh
cd ..

5^th - Execute the lysozyme_in_water application

There are three versions of the lysozyme_in_water application:

5.1 Bare: Sequential implementation as a bash script using the building blocks directly.

cd application/Bare
./steps.sh
# Check output folder (use "grace" to visualize xvg files).
cd ../..

5.2 SnakeMake: Parallelized with SnakeMake.

cd application/SnakeMake
snakemake Snakefile
# Check output folder (use "grace" to visualize xvg files).
cd ../..

5.3 PyCOMPSs: Parallelized with PyCOMPSs.

cd application/PyCOMPSs
./launch.sh
# Check output folder (use "grace" to visualize xvg files).
cd ../..

License

Apache 2.0

Contact

https://permedcoe.eu/contact/

This software has been developed for the PerMedCoE project, funded by the European Commission (EU H2020 951773).