Singularity container for molecular electrostatic calculations using PDB2PQR/APBS and Brownian dynamics with BrownDye.
This singularity image contains a complete software environment for running BrownDye (version 1 and 2) simulations. It also includes PDB2PQR and APBS.
Please register your use of APBS and PDB2PQR.
The image has been verified to work on XSEDE comet and TSCC shared cluster at SDSC. It will automatically bind /cvmfs /oasis /projects /scratch directories, if available on the host.
Pull the singularity image:
singularity pull shub://nbcrrolls/electrostatics-singularity
Start bash shell in the container:
singularity shell nbcrrolls-electrostatics-singularity-master-latest.simg
Now the container is running and we can start a BrownDye2 job (using the Thrombin example):
module load browndye2
cp -ai $BD2_PATH/examples/thrombin .
cd thrombin
sed -i 's/-PE0//g' *
sed -i 's/<n_trajectories> 10000 /<n_trajectories> 1000 /' t_m_simulation.xml.bak
make all # takes about min to run
module unload browndye2
And if you want to use BrownDye version 1:
module load browndye1
cp -ai $BD1_PATH/thrombin-example .
cd thrombin-example
sed -i 's/-PE0//g' *
sed -i 's/<n-trajectories> 10000 /<n-trajectories> 1000 /' input.xml.bak # limit the number of calculated trajectories
make all
bd_top input.xml
nam_simulation t-m-simulation.xml # this takes about 3 min to run
cat results.xml
module unload browndye1
After we are finished we can quit the container:
exit
You can also access individual applications from the electrostatics container.
To list available applications:
$ singularity apps nbcrrolls-electrostatics-singularity-master-latest.simg
apbs
pdb2pqr
nam_simulation
we_simulation
To run, for example, apbs calculation:
singularity exec nbcrrolls-electrostatics-singularity-master-latest.simg apbs input.in
or
singularity run --app apbs nbcrrolls-electrostatics-singularity-master-latest.simg input.in
This Singularity image is hosted on Singularity Hub:
