Gromacs for Analysis
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 tutorial, our focus will be on running Gromacs package with Bacalhau
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 usespc
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:
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