Open-Omics-Gromacs

Open-Omics-Gromacs is a dockerized GROMACS setup for high-performance molecular dynamics simulations. It uses multi-threading and Intel MKL FFT for enhanced computational efficiency on modern Intel CPUs.

Docker Setup Instructions

1. Build the Docker Image

If Your Machine Uses a Proxy

In some cases, systems within a corporate or institutional network require a proxy to connect to the internet. To enable internet connectivity during the Docker build process, specify the proxy environment variables (http_proxy, https_proxy, and no_proxy) during the docker build process.

docker build --build-arg http_proxy=<http_proxy> --build-arg https_proxy=<https_proxy> --build-arg no_proxy=<no_proxy_ip> -t grms_dock .

Example Proxy Variables:

http_proxy=http://proxy.example.com:port
https_proxy=http://proxy.example.com:port
no_proxy=localhost,127.0.0.1,.example.com

If Your Machine Doesnot Use Proxy:

docker build -t grms_dock .

After successfully building the Docker image, verify its presence:

docker images |  grep grms_dock

2. Prepare Input and Output Directories

After Building docker image, set up the necessary input and output directories:

Steps:

1) If you already have a protein PDB file, you can use it for GROMACS simulation. Otherwise, you can download a sample protein PDB file using the following command:

wget https://files.rcsb.org/download/1AKI.pdb

2) Create a directory for storing simulation output:

mkdir -p grms_output

3) Set environment variables for easy access to input and output directories:

export INPUT_GMX_CPU=$PWD/grms_input
export OUTPUT_GMX_CPU=$PWD/grms_output

4) Prepare Input Directory (grms_input) with Necessary Files:
Copy the following files to the grms_input directory:

  • .mdp files: These are already provided to define simulation parameters.
  • <protein_name>.pdb: Replace protein_name with the name of the downloaded PDB file or your own PDB file.
  • run_commands.sh: The script used to run the complete workflow of the simulation process. 5) Set appropriate permissions: 
    chown -R 1001:1001 $INPUT_GMX_CPU
chown -R 1001:1001 $OUTPUT_GMX_CPU
chmod -R a+w $OUTPUT_GMX_CPU
chmod +x grms_input/run_commands.sh

3. Run the Docker Container

Run Complete Workflow with a Selected PDB File

docker run -v $INPUT_GMX_CPU:/input -v $OUTPUT_GMX_CPU:/output -it grms_dock <protein_name>.pdb

Explanation:

  • -v $INPUT_GMX_CPU:/input mounts the local input directory to /input inside the container.
  • -v $OUTPUT_GMX_CPU:/output mounts the local output directory to /output inside the container.
  • <protein_name>.pdb is the selected PDB file for simulation.

Note: If you encounter errors related to missing atoms, non-standard residues, incomplete terminal groups, residue numbering, or naming mismatches during the pdb2gmx stage in GROMACS, PDBFixer(https://github.com/openmm/pdbfixer) is a helpful tool that can clean and fix PDB files before passing them to GROMACS. Additionally, pay close attention to warnings and notes from GROMACS, as they often provide valuable insights and indicate necessary modifications for a successful run.

Run an Individual GROMACS Command

GROMACS command line utilities can be called directly using our docker container in the following way:

docker run -v $INPUT_GMX_CPU:/input -v $OUTPUT_GMX_CPU:/output -it grms_dock gmx <command>

EXAMPLE

docker run -v $INPUT_GMX_CPU:/input -v $OUTPUT_GMX_CPU:/output -it grms_dock gmx pdb2gmx

For detailed command usage, visit (https://manual.gromacs.org/documentation/current/onlinehelp/).

4. Access Simulation Results

Once the simulation completes, access the results:

ls $OUTPUT_GMX_CPU

This directory contains all output data for the md01 stage of the complete workflow simulation. For individual command runs, everything will be stored in the grms_input directory.

The Original README for Gromacs starts here:

Welcome to the official version of GROMACS!

If you are familiar with Unix, it should be fairly trivial to compile and install GROMACS. GROMACS uses only the CMake build system, and our installation guide can be found at http://manual.gromacs.org/documentation/current/install-guide/index.html

Visit http://forums.gromacs.org/ for discussions and advice. Report bugs at https://gitlab.com/gromacs/gromacs/-/issues Of course we will do our utmost to help you with any problems, but PLEASE READ THE INSTALLATION INSTRUCTIONS BEFORE CONTACTING US!

There are also several other online resources available from the homepage, and special information for developers.

If you use GROMACS for research (or other purposes) make sure to reference the correct version of the code. The CITATION.cff file next to this README contains all metadata useful for citation.

If you are a developer, or change the source for any other reason, check out http://www.gromacs.org/development.

GROMACS is free software, distributed under the GNU Lesser General Public License, version 2.1 However, scientific software is a little special compared to most other programs. Both you, we, and all other GROMACS users depend on the quality of the code, and when we find bugs (every piece of software has them) it is crucial that we can correct it and say that it was fixed in version X of the file or package release. For the same reason, it is important that you can reproduce other people’s result from a certain GROMACS version.

The easiest way to avoid this kind of problems is to get your modifications included in the main distribution. We’ll be happy to consider any decent code. If it’s a separate program it can probably be included in the contrib directory straight away (not supported by us), but for major changes in the main code we appreciate if you first test that it works with (and without) MPI, threads, double precision, etc.

If you still want to distribute a modified version or use part of GROMACS in your own program, remember that the entire project must be licensed according to the requirements of the LGPL v2.1 license under which you received this copy of GROMACS. We request that it must clearly be labeled as derived work. It should not use the name “official GROMACS”, and make sure support questions are directed to you instead of the GROMACS developers. Sorry for the hard wording, but it is meant to protect YOUR research results!

The development of GROMACS is mainly funded by academic research grants. To help us fund development, we humbly ask that you cite the GROMACS papers:

  • GROMACS: A message-passing parallel molecular dynamics implementation H.J.C. Berendsen, D. van der Spoel and R. van Drunen Comp. Phys. Comm. 91, 43-56 (1995) DOI: https://doi.org/10.1016/0010-4655(95)00042-E

  • GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl J. Chem. Theory Comput. 4 (2008) pp. 435-447 DOI: https://doi.org/10.1021/ct700301q

  • GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit Sander Pronk, Szilárd Páll, Roland Schulz, Per Larsson, Pär Bjelkmar, Rossen Apostolov, Michael R. Shirts, Jeremy C. Smith, Peter M. Kasson, David van der Spoel, Berk Hess, Erik Lindahl. Bioinformatics 29 (2013) pp. 845-54 DOI: https://doi.org/10.1093/bioinformatics/btt055

  • Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS Szilárd Páll, Mark J. Abraham, Carsten Kutzner, Berk Hess, Erik Lindahl In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale, Lecture Notes for Computer Science, 8759 (2015) pp. 3–27 DOI: https://doi.org/10.1007/978-3-319-15976-8_1

  • GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E. Lindahl, SoftwareX, 1, (2015), 19-25 DOI: https://doi.org/10.1016/j.softx.2015.06.001

There are a lot of cool features we’d like to include in future versions, but our resources are limited. All kinds of donations are welcome, both in form of code, hardware and funding! Industrial users who choose to pay for a license pro bono (it is still LGPL and can be redistributed freely) or contribute in other ways are listed as GROMACS supporters on our webpages. Don’t hesitate to contact us if you are interested.