Molecular Dynamics Simulations TSD Journal

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Prepare the local environment on the LRZ: <source lang="bash"> module load git git clone git:// PATH=$PATH:/home/hpc/pr58ni/di34fod/mapra/AGroS/ export PATH cd AGroS/ wget chmod +x installscwrl4 ./installscwrl4 ln -s Scwrl4 scwrl </source>

After that, the necessary structure files can be retrieved from the biolab ressources with

Simulations is a simple test script to test whether all parameters are correct and similar things. Note that the number of cores has to be reduced to 16 on the mpp1_inter queue. Since the wild-type simulation still ran into errors, the number of cores was reduced to 12, according to the Gromacs manual. are the final scripts for the production runs. The number of cores was increased to 32 for the two mutations, but left at 12 for the wild-type.