Molecular Dynamics Simulation of ARSA

Preparation

To prepare the pdb-structure for th molecular dynamics simulation we did all steps mentioned in the task-description and also did 5 rounds of minimization with minimise.

local preparation with gromacs

To prepare the structure for the long minimization-runs we wrote two scripts. (TODO: include scripts from virtualBox)

LRZ-runs with gromacs

To run gromacs on the LRZ-cluster we used the following config-file: (TODO: include working config-file)