Difference between revisions of "Molecular Dynamics Simulations TSD Journal"
| (One intermediate revision by the same user not shown) | |||
| Line 1: | Line 1: | ||
Back to [[Molecular_Dynamics_Simulations_TSD|discussion page]]. |
Back to [[Molecular_Dynamics_Simulations_TSD|discussion page]]. |
||
| + | ==Preparation== |
||
Prepare the local environment on the LRZ: |
Prepare the local environment on the LRZ: |
||
<source lang="bash"> |
<source lang="bash"> |
||
| + | module load git |
||
git clone git://github.com/offmarc/AGroS.git |
git clone git://github.com/offmarc/AGroS.git |
||
PATH=$PATH:/home/hpc/pr58ni/di34fod/mapra/AGroS/ |
PATH=$PATH:/home/hpc/pr58ni/di34fod/mapra/AGroS/ |
||
| Line 13: | Line 15: | ||
</source> |
</source> |
||
| − | After that, the necessary structure files can be retrieved from the biolab ressources with [https://gist.github.com/3019558 getStructures.sh]. |
+ | After that, the necessary structure files can be retrieved from the biolab ressources with [https://gist.github.com/3019558 getStructures.sh]. |
| + | |||
| + | ==Simulations== |
||
| + | [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]. |
||
<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. |
<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. |
||
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.
