👩‍💻 I'm working on it, so please be patient.

Introduction

nf-core/moleculardynamics is a bioinformatics pipeline for running molecular dynamic simulations (MD) using GROMACS open-source software. This workflow enables researchers to perform standard protein simulations in a fully automated manner, with minimal configuration, on both local and high-performance computing (HPC) environments.

We are currently working on the following tasks:

1. 🚀📆 Official release of the nf-core/moleculardynamics pipeline.
2. 🛠👩‍💻 Expanding the pipeline’s capabilities to include more analysis modules (e.g., RMSF, distances), and integrating specialized tools for membrane proteins and protein-ligand complexes.
3. 📚📝 Generating a comprehensive test dataset.

Pipeline

The nf-core/moleculardynamics pipeline automates a standard GROMACS MD simulation workflow. The major steps are:

• Input pre-processing: From the PDB structure, remove the missing atoms.
• Production run: Main subworkflow of the pipeline.
  • Generation of molecular topology,
  • System solvation, and ion addition to neutralize the system.
  • Energy Minimization: Removal of steric clashes and relaxation of the initial structure.
  • Equilibration: NVT (constant Number, Volume, Temperature) and NPT (constant Number, Pressure, Temperature) equilibration to bring the system to the desired temperature and density.
  • Production MD: Execution of the main molecular dynamics simulation.
• Post-processing: Centering the protein and remove periodic boundary condition (PBC).
• Analysis: Preliminary analysis of the Root-Mean-Square Deviation (RMSD).

Usage

[👩‍💻 working on it]

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

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To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

Credits

nf-core/moleculardynamics has been developed by Sara Tolosa Alarcón (@sarata00) from the Computational Biology Group at the Barcelona Supercomputing Center under the deCYPher project and supervision of Miguel Romero-Durana (@migromero).

Contributions and Support

[👩‍💻 working on it]

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch on the Slack #moleculardynamics channel (you can join with this invite).

Citations

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An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.