Difference between revisions of "Molecular Dynamics Simulations TSD Journal"
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Back to [[Molecular_Dynamics_Simulations_TSD|discussion page]]. |
Back to [[Molecular_Dynamics_Simulations_TSD|discussion page]]. |
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| + | ==Preparation== |
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| + | Prepare the local environment on the LRZ: |
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| + | <source lang="bash"> |
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| + | module load git |
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| + | git clone git://github.com/offmarc/AGroS.git |
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| + | PATH=$PATH:/home/hpc/pr58ni/di34fod/mapra/AGroS/ |
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| + | export PATH |
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| + | cd AGroS/ |
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| + | wget http://dunbrack.fccc.edu/scwrl4/license/tempToDownload_76395/Jonas_Reeb_632385309/stat_scwrl4_lin.php |
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| + | chmod +x installscwrl4 |
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| + | ./installscwrl4 |
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| + | ln -s Scwrl4 scwrl |
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| + | </source> |
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| + | |||
| + | After that, the necessary structure files can be retrieved from the biolab ressources with [https://gist.github.com/3019558 getStructures.sh]. |
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| + | |||
| + | ==Simulations== |
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| + | [https://gist.github.com/3019572 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 [http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm Gromacs manual]. |
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| + | <br/>[https://gist.github.com/3019579 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. |
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Latest revision as of 18:54, 29 June 2012
Back to discussion page.
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.
