README.md

Docker container for molecular electrostatic calculations using PDB2PQR/APBS and Brownian dynamics with BrownDye.

This docker image contains a complete software environment for running BrownDye (version 2) simulations. It also includes PDB2PQR and APBS.

Please register your use of APBS and PDB2PQR and at https://browndye.ucsd.edu/ for use of BrownDye.

Using the container

Pull the docker image:

docker pull rokdev/bddocker:latest

Start the container in the current directory:

docker run --rm -ti -u 1000:1000 -v "$PWD":/home/browndye/data \
 -w /home/browndye/data rokdev/bddocker:latest

Now the container is running and we can start a BrownDye2 simulation (using the Thrombin example):

cp -ai $BD2_PATH/examples/thrombin .
cd thrombin
sed -i 's/<n_trajectories> 1000 /<n_trajectories> 100 /' input.xml.bak
make all
bd_top input.xml
nam_simulation thrombin_tmodulin_simulation.xml # takes about 4 min to run
cat results.xml

After we are finished we can quit the container:

exit

Latest docker images builds can be seen on Docker Hub.

This project is supported by a grant from the National Institutes of Health.