Gromacs for Analysis

Introduction

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

TD;LR

Running Gromacs package with Bacalhau

Downloading datasets

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”

input
└── 1AKI.pdb

Uploading the datasets

Upload the directory to IPFS using IPFS CLI (Installation Instructions) [Not recommended]

$ ipfs add -r input/
added QmTCCqPzX3qSJHuMeSma9uCqUnriZ5eJX7MnxebxydL89f input/1AKI.pdb
added QmeeEB1YMrG6K8z43VdsdoYmQV46gAPQCHotZs9pwusCm9 input
 113.59 KiB / 113.59 KiB [============================================================================================] 100.00%

Copy the CID in the end which is QmeeEB1YMrG6K8z43VdsdoYmQV46gAPQCHotZs9pwusCm9 Upload the directory to IPFS using Pinata (Recommended)

Running Bacalhau Job

This command converts coordinate files to topology and FF-compliant coordinate files:

bacalhau docker run \
-i ipfs://QmeeEB1YMrG6K8z43VdsdoYmQV46gAPQCHotZs9pwusCm9:/input \
gromacs/gromacs \
-- /bin/bash -c 'echo 15 | gmx pdb2gmx -f input/1AKI.pdb -o outputs/1AKI_processed.gro -water spc'

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

%%bash
curl -sL https://get.bacalhau.org/install.sh | bash

Your system is linux_amd64
No BACALHAU detected. Installing fresh BACALHAU CLI...
Getting the latest BACALHAU CLI...
Installing v0.2.3 BACALHAU CLI...
Downloading https://github.com/filecoin-project/bacalhau/releases/download/v0.2.3/bacalhau_v0.2.3_linux_amd64.tar.gz ...
Downloading sig file https://github.com/filecoin-project/bacalhau/releases/download/v0.2.3/bacalhau_v0.2.3_linux_amd64.tar.gz.signature.sha256 ...
Verified OK
Extracting tarball ...
NOT verifying Bin
bacalhau installed into /usr/local/bin successfully.
Client Version: v0.2.3
Server Version: v0.2.3

%%bash --out job_id
bacalhau docker run \
--id-only \
--wait \
--timeout 3600 \
--wait-timeout-secs 3600 \
-i ipfs://QmeeEB1YMrG6K8z43VdsdoYmQV46gAPQCHotZs9pwusCm9:/input \
gromacs/gromacs
-- /bin/bash -c 'echo 15 | gmx pdb2gmx -f input/1AKI.pdb -o outputs/1AKI_processed.gro -water spc'

%env JOB_ID={job_id}

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:

%%bash
bacalhau list --id-filter ${JOB_ID} --wide

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:

%%bash
bacalhau describe ${JOB_ID}

To Download the results of your job, run the following command:

%%bash
rm -rf results && mkdir -p results
bacalhau get $JOB_ID --output-dir results

After the download has finished you should see the following contents in the results directory

%%bash
ls results/

The Rach repository contains self-explanatory results.