Installation of GENESIS for Tutorials

Preparation of the directory

First, let’s create a working directory for the GENESIS tutorials under your home directory (/home/username/) by executing the following commands. We will set up a main directory named GENESIS_Tutorials-2022, and inside it, create two subdirectories: Programs and Data.

  • Programs will store the main software used in this project, such as the GENESIS executable.
  • Data will store external resources that are commonly used throughout the tutorials, including PDB files (see Tutorial 2.1) and force field parameter files (see Tutorial 2.2).

Therefore, within the Data directory, we will also create two subdirectories: PDB and Parameters.

For downloading the actual tutorial materials, we will use Git to clone the repository into a subdirectory named genesis_tutorial_materials (starting from Tutorial 3 onward).

# Move to the home directory 
$ cd
$ pwd
/home/username

# Create a directory for this project
$ mkdir GENESIS_Tutorials-2022
$ cd GENESIS_Tutorials-2022

# Create main directories
$ mkdir Programs Data
$ git clone https://github.com/genesis-release-r-ccs/genesis_tutorial_materials
$ ls
Data  Programs  genesis_tutorial_materials

# Create sub-directories
$ mkdir Data/PDB
$ mkdir Data/Parameters

Download GENESIS

These tutorials were originally developed using GENESIS version 2.0.0. However, they are expected to be compatible with all releases in the GENESIS 2.x series.

Let’s download and put the GENESIS source code in Programs:

# Put the source code of GENESIS in the "Programs" directory 
$ cd Programs
$ git clone https://github.com/genesis-release-r-ccs/genesis.git
$ cd genesis

# Optional
$ git checkout v2.0.0

Install GENESIS

Now, let’s run the configure command. This script automatically checks your computing environment and generates a Makefile with appropriate compilation options for your system.

If you encounter any issues during this process, please refer to the GENESIS user manual or visit the Installation guide for troubleshooting tips.

Once configure completes successfully, compile and install the program using make and make install.

This will create a bin directory in your current location and install the compiled programs there. After installation, you will find several executables in the bin directory. Among them, atdyn and spdyn are the main MD programs. The rest are auxiliary tools for trajectory analysis.

Starting from Tutorial 3, we will use many of these tools throughout our simulations and analyses.

# Install GENESIS
$ ./configure
$ make
$ make install

Here, we did not add any options to the configure command. This simple command will install GENESIS running on a CPU. In fact, most tutorials are designed to use the CPU version. If you want to run the tutorials using CPU+GPU, please add the options for GPU. However, note that in this case only spdyn will be installed, and some tutorials cannot be run with spdyn alone.

In the example above, we did not specify any options with the configure command. This default setup installs the CPU version of GENESIS, which is sufficient for most of the tutorials in this series.

If you wish to run GENESIS using both CPU and GPU, please refer to the GPU installation options and add the appropriate flags during configuration.

Note: When using the GPU option, only the spdyn program will be installed. Some tutorials in this series require the atdyn program and therefore cannot be completed with spdyn alone. Be sure to choose the installation method that matches your needs.

Let’s check the directory

Now, we have constructed the following directory structure:

/home/username
+ GENESIS_Tutorials-2022  # Project name
    |
    + Programs           # Main software for this project
    |  + genesis
    |     + src          # Source code of GENESIS 2.0.0
    |     + bin          # Binary code of GENESIS 2.0.0
    |     + doc          # User manual of GENESIS 2.0.0
    |     + tests        # Regression tests
    |     + ...
    |
    + Data               # External data of this project
    |  + PDB
    |  + Parameters
    |
    + genesis_tutorial_materials  # Simulation materials
    |  + tutorial_2.3
    |  + tutorial_3.1
    |  + tutorial_3.2
    |  + ...

A Note on Installation and Directory Organization

Some users may wish to install programs in system-wide directories such as /usr/local/bin. However, this approach can make it difficult to trace where the original source code resides, especially in large collaborative projects. To avoid such confusion, we recommend installing all software locally, within the project directory.

In our tutorial, we created a Data directory to store all external input files. This includes files such as PDB structures, force field parameters, and other reference data. Keeping these files in a dedicated Data directory helps to clearly distinguish input data from the results and ensures that you can easily track what was used during simulations. In real research scenarios, this could include unpublished PDB files provided by collaborators — and it’s especially important to preserve their integrity. Storing them in a dedicated location helps avoid accidental overwrites or modifications.

Why Good Directory Hygiene Matters

Throughout this tutorial series, we will also introduce simple techniques to keep your project directory clean and well-organized. In computational research, large numbers of files are often generated automatically. Without a clear and consistent directory structure, it’s easy for things to get messy — leading to:

  • Confusion and mistakes in simulation or analysis steps
  • Difficulty in writing reports or publications
  • Poor reproducibility and data traceability
  • Frustration when handing the project off to other team members

A cluttered directory is not just inconvenient — it can also hinder your ability to publish results effectively.

By following the practices shown in this tutorial, we hope you will develop good habits for managing your research data and code, helping to maintain both scientific rigor and collaborative efficiency.

Written by Takaharu Mori@RIKEN Theoretical Molecular Science Laboratory, Dec. 16, 2021
Edited by Cheng Tan@RIKEN Center for Computational Science, Jun. 05, 2025

Updated: