Gromacs for Analysis
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GROMACS is a package for high-performance molecular dynamics and output analysis. Molecular dynamics is a computer simulation method for analyzing the physical movements of atoms and molecules
In this example, we will make use of program to add hydrogens to the molecules and generates coordinates in Gromacs (Gromos) format and topology in Gromacs format.
In this example tutorial, our focus will be on running Gromacs package with Bacalhau
To get started, you need to install the Bacalhau client, see more information
Datasets can be found here , In this example we use dataset. After downloading, place it in a folder called “input”
The simplest way to upload the data to IPFS is to use a third-party service to "pin" data to the IPFS network, to ensure that the data exists and is available. To do this you need an account with a pinning service like or . Once registered you can use their UI or API or SDKs to upload files.
Alternatively, you can upload your dataset to IPFS using :
Copy the CID in the end which is QmeeEB1YMrG6K8z43VdsdoYmQV46gAPQCHotZs9pwusCm9
Let's run a Bacalhau job that converts coordinate files to topology and FF-compliant coordinate files:
Lets look closely at the command above:
bacalhau docker run: call to Bacalhau
-i ipfs://QmeeEB1YMrG6K8z43VdsdoYmQV46gAPQCHotZs9pwusCm9:/input: here we mount the CID of the dataset we uploaded to IPFS to use on the job
-f input/1AKI.pdb: input file
-o outputs/1AKI_processed.gro: output file
-water Water model to use. In this case we use spc
When a job is submitted, Bacalhau prints out the related job_id. We store that in an environment variable so that we can reuse it later on.
The job description should be saved in .yaml format, e.g. gromacs.yaml, and then run with the command:
Job status: You can check the status of the job using bacalhau job list.
When it says Published or Completed, that means the job is done, and we can get the results.
Job information: You can find out more information about your job by using bacalhau job describe.
Job download: You can download your job results directly by using bacalhau job get. Alternatively, you can choose to create a directory to store your results. In the command below, we created a directory (results) and downloaded our job output to be stored in that directory.
To view the file, run the following command:
gromacs/gromacs: we use the official
gmx pdb2gmx: command in GROMACS that performs the conversion of molecular structural data from the Protein Data Bank (PDB) format to the GROMACS format, which is used for conducting Molecular Dynamics (MD) simulations and analyzing the results. Additional parameters could be found here
For a similar tutorial that you can try yourself, check out
The same job can be presented in the format. In this case, the description will look like this:
If you have questions or need support or guidance, please reach out to the (#general channel).