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 gmx pdb2gmx program to add hydrogens to the molecules and generates coordinates in Gromacs (Gromos) format and topology in Gromacs format
Running Gromacs package with Bacalhau
Datasets can be found here https://www.rcsb.org, In this example we use RCSB PDB - 1AKI dataset. After downloading place it in a folder called “input”
Upload the directory to IPFS using IPFS CLI (Installation Instructions) [Not recommended]
Copy the CID in the end which is QmeeEB1YMrG6K8z43VdsdoYmQV46gAPQCHotZs9pwusCm9 Upload the directory to IPFS using Pinata (Recommended)
This command converts coordinate files to topology and FF-compliant coordinate files:
Lets look at the command above more closely:
bacalhau docker run using the docker backend
-i ipfs://QmeeEB1YMrG6K8z43VdsdoYmQV46gAPQCHotZs9pwusCm9:/input here we mount the CID of the dataset we uploaded to IPFS and mount it to a folder called data on the container
gromacs/gromacs we use the official gromacs - Docker Image
-f input/1AKI.pdb input file
-o output/1AKI_processed.gro output file
-water Water model to use in this case we use spc
Additional parameters could be found here gmx pdb2gmx — GROMACS 2022.2 documentation
(similar tutorial you can try yourself KALP-15 in DPPC - GROMACS Tutorial )
Installing Bacalhau
Running the commands will output a UUID. This is the ID of the job that was created. You can check the status of the job with the following command:
Where it says Completed, that means the job is done, and we can get the results.
To find out more information about your job, run the following command:
To Download the results of your job, run the following command:
After the download has finished you should see the following contents in the results directory
The Rach repository contains self-explanatory results.
