Difference between revisions of "Task8 Hemochromatosis Protocol"
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Bernhoferm (talk | contribs) (→Let's get serious) |
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note: --partition=mpp1_inter means this is for the test runs! |
note: --partition=mpp1_inter means this is for the test runs! |
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| + | <br style="clear:both;"> |
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| + | == Let's get serious == |
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| + | Final script for one of the MDS runs (in this case the native protein): |
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| + | #!/bin/bash |
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| + | #SBATCH -o /home/hpc/pr58ni/di34fol/masterprakt/task8/jobs/log/1a6zC.%j.%N.log |
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| + | #SBATCH -D /home/hpc/pr58ni/di34fol/masterprakt/task8/models/ |
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| + | #SBATCH -J 1a6zC_MD |
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| + | #SBATCH --clusters=mpp1 |
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| + | #SBATCH --get-user-env |
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| + | #SBATCH --ntasks=16 |
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| + | #SBATCH --mail-type=end |
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| + | #SBATCH --mail-user=MichaelBernhofer@gmx.de |
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| + | #SBATCH --export=NONE |
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| + | #SBATCH --time=32:00:00 |
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| + | source /etc/profile.d/modules.sh |
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| + | module load gromacs |
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| + | export PATH=$PATH:/home/hpc/pr58ni/di34fol/masterprakt/task8/AGroS/ |
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| + | AGroS 1a6zC.pdb -dir /home/hpc/pr58ni/di34fol/masterprakt/task8/models/1a6zC/ -threads 16 -v |
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Latest revision as of 12:57, 2 July 2012
Contents
Getting started
Setting up AGroS
Get AGroS:
module load git git clone git://github.com/offmarc/AGroS.git
Add line to .profile
export PATH=$PATH:$HOME/masterprakt/task8/AGroS/
Setting up SCWRL4
Install SCWRL4 into AGroS directory. Add link from "scwrl" to "Scwrl4" (otherwise AGroS won't find it).
ln -s Scwrl4 scwrl
Sample script
#!/bin/bash #SBATCH -o /home/hpc/pr58ni/di34fol/masterprakt/task8/jobs/log/1a6zC.%j.%N.log #SBATCH -D /home/hpc/pr58ni/di34fol/masterprakt/task8/models/ #SBATCH -J 1a6zC_MD #SBATCH --partition=mpp1_inter #SBATCH --get-user-env #SBATCH --ntasks=16 #SBATCH --mail-type=end #SBATCH --mail-user=MichaelBernhofer@gmx.de #SBATCH --export=NONE #SBATCH --time=02:00:00 source /etc/profile.d/modules.sh module load gromacs export PATH=$PATH:/home/hpc/pr58ni/di34fol/masterprakt/task8/AGroS/ AGroS 1a6zC.pdb -dir /home/hpc/pr58ni/di34fol/masterprakt/task8/models/1a6zC/ -threads 16 -v
note: --partition=mpp1_inter means this is for the test runs!
Let's get serious
Final script for one of the MDS runs (in this case the native protein):
#!/bin/bash #SBATCH -o /home/hpc/pr58ni/di34fol/masterprakt/task8/jobs/log/1a6zC.%j.%N.log #SBATCH -D /home/hpc/pr58ni/di34fol/masterprakt/task8/models/ #SBATCH -J 1a6zC_MD #SBATCH --clusters=mpp1 #SBATCH --get-user-env #SBATCH --ntasks=16 #SBATCH --mail-type=end #SBATCH --mail-user=MichaelBernhofer@gmx.de #SBATCH --export=NONE #SBATCH --time=32:00:00 source /etc/profile.d/modules.sh module load gromacs export PATH=$PATH:/home/hpc/pr58ni/di34fol/masterprakt/task8/AGroS/ AGroS 1a6zC.pdb -dir /home/hpc/pr58ni/di34fol/masterprakt/task8/models/1a6zC/ -threads 16 -v
