To run our jobs we need input data from the Max Planck Institue in Göttingen (mpibpc.mpg.de/grubmueller).
We are going to download two systems as potential input data.
sudo yum install -y bsdtar mkdir -p /fsx/input/gromacs wget -qO- https://www.mpibpc.mpg.de/15101328/benchRIB.zip |bsdtar xf - -C /fsx/input/gromacs wget -qO- https://www.mpibpc.mpg.de/15101317/benchMEM.zip |bsdtar xf - -C /fsx/input/gromacs
The MEM benchmark system is an aquaporin tetramer embedded in a lipid membrane surrounded by water and ions, comprising 81 thousand atoms altogether.
The RIB benchmark is a 2 M atoms large MD system of a ribosome surrounded by water and ions.