The Molecular Simulation Pipeline simplifies molecular dynamics simulations with GROMACS and dockings with AutoDock Vina. Therefore it facilitates the communication to a computational cluster and performs simulations on it with simple commands. Further, it provides some analysis methods.

• GROMACS
• AutoDock Vina
• MGLTools
• PyMOL (Open Source)

• Established passwordless ssh login
• qsub command for queueing scripts
• qstat to obtain queue stats

• GROMACS
• MGLTools
• PyMOL (Open Source)
• GNUPlot
• python3

git clone https://github.com/ortzt/MolSimPipeline.git

• In the file 'main.sh' the servername (server='[email protected]') and the absolute path to the working directory on the server (servpath='/root/path/on/server/to/working/dir') must be changed.
• A Username directory must exist or manually created in the working directory on the server

cd into the MolSimPipeline directory and run the script with ./main.sh. For the usage visit the USAGE file.