Help - Frequently Asked Questions


BioBB Workflows is a platform offering a web-based Graphical User Interface (GUI) on top of a collection of transversal biomolecular simulation workflows built using the BioExcel Building Blocks library (BioBB), including Molecular Dynamics (MD) setup, protein-ligand docking or MD trajectory analysis. It has been designed from the expertise gained with similar and acclaimed projects such as MDWeb (reference) or NAFlex (reference)).

  • BioBB Workflows offers a set of pre-configured biomolecular simulation workflows with which you can:
    • Prepare a protein or nucleic acid structure to run a Molecular Dynamics simulation with GROMACS or AMBER MD packages (MD Setup), including ligands.
    • Run a production MD simulation in HPC resources from the GUI (only available if HPC credentials are previously configured in the web server).
    • Model protein or nucleic acid mutations on the 3D structures.
    • Parameterize a small molecule for GROMACS, AMBER or CNS/XPLOR MD packages.
    • Run a protein-ligand docking process.
    • Run MD trajectory analyses.
  • Workflows can be run in the BioBB Workflows computational resources (with limited configuration parameters) or can be downloaded and run in the user own premises (with complete flexibility with configuration parameters). Workflows are offered in two different programming workflow languages: Python and CWL.
  • BioBB Workflows MD Setup pipelines are designed to prepare basic structures (protein, nucleic acids) and complexes (protein-ligand/s, protein-DNA, protein-RNA) for classical MD systems.
  • BioBB Workflows MD Setup pipelines are NOT designed to prepare advanced structures (e.g. ionic coordinations, modified –covalently-bonded- amino acids, covalently-bonded ligands).
  • BioBB Workflows MD Setup pipelines are NOT designed to prepare structures for biased MD systems (e.g. Replica Exchange MD, Targeted MD, Steered MD, Metadynamics).
  • Start a new Project: Menu Create Project From Structure.
  • Upload or find your interested structure (Step 1: Provide Structure).
  • Check for possible issues with the web server Graphical User Interface. Upload ligand parameters if needed. (Step 2: Check Structure).
  • Choose the most appropriate workflow for your particular project (check the Workflows help section). IMPORTANT: Click the checkbox to prepare configuration files to run a long MD simulation in your own premises and change parameters accordingly (Step 3: Settings).
  • Run a BioBB Workflows MD Setup pipeline (Step 4: Run Project).
  • Download results of the workflow from the Project Actions section.
  • Open the file and follow the instructions to run a production MD simulation with the prepared system (downloaded files).
  • Unfortunately not. BioBB Workflows web server is designed to prepare MD systems (MD setup), but not to run a production (long) MD. The computational resources behind the server are not enough for that. The longest MD simulation allowed is a 1ns simulation (included as a last step of the AMBER MD Setup workflow).
  • However, extend the simulation in users machines can be easily done just following the instructions provided in the file included with the set of downloadable files generated by all the different MD Setup workflows.
  • Besides, if you have access to one of the BioBB Workflows compatible HPC supercomputers (see corresponding help section), the production MD simulation can be launched directly from the web server to the supercomputer, after properly configuring ssh keys in the user’s profile (see corresponding help section).

Please visit the Workflows - Help section of this same website:

BioBB Workflows Workflows

No, the BioBB Workflows website is public and open access, but in case you want to enjoy some advantages such as run HPC, private projects, persistent projects, rerun projects or clone projects then you should register to the website. For more information about the process of registering, please visit the Personal Area - Help section of this same website:

BioBB Workflows personal area