Molecular Dynamics Simulations TSD Journal

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Preparation

Prepare the local environment on the LRZ: <source lang="bash"> module load git git clone git://github.com/offmarc/AGroS.git PATH=$PATH:/home/hpc/pr58ni/di34fod/mapra/AGroS/ export PATH cd AGroS/ wget http://dunbrack.fccc.edu/scwrl4/license/tempToDownload_76395/Jonas_Reeb_632385309/stat_scwrl4_lin.php chmod +x installscwrl4 ./installscwrl4 ln -s Scwrl4 scwrl </source>

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

Simulations

run_test.sh 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.
run_production.sh 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.