Difference between revisions of "Task8 Hemochromatosis Protocol"

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Install SCWRL4 into AGroS directory.
  
Install SCWRL4 into AGroS directory.
 
Add link from "scwrl" to "Scwrl4" (otherwise AGroS won't find it).
  
Add link from "scwrl" to "Scwrl4" (otherwise AGroS won't find it).
−
ln -s scwrl Scwrl4
 +
ln -s Scwrl4 scwrl
  +
  +
  +
<br style="clear:both;">
  +
  +
=== 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=$PATH:/home/hpc/pr58ni/di34fol/masterprakt/task8/AGroS/
  +
AGroS 1a6zC.pdb -dir /home/hpc/pr58ni/di34fol/masterprakt/task8/models/1a6zC/ -threads 16 -v
  +
  +
note: --partition=mpp1_inter means this is for the test runs!
  +
  +
<br style="clear:both;">
  +
  +
== Let's get serious ==
  +
  +
  +
Final script for one of the MDS runs (in this case the native protein):
  +
#!/bin/bash
  +
#SBATCH -o /home/hpc/pr58ni/di34fol/masterprakt/task8/jobs/log/1a6zC.%j.%N.log
  +
#SBATCH -D /home/hpc/pr58ni/di34fol/masterprakt/task8/models/
  +
#SBATCH -J 1a6zC_MD
  +
#SBATCH --clusters=mpp1
  +
#SBATCH --get-user-env
  +
#SBATCH --ntasks=16
  +
#SBATCH --mail-type=end
  +
#SBATCH --mail-user=MichaelBernhofer@gmx.de
  +
#SBATCH --export=NONE
  +
#SBATCH --time=32:00:00
  +
source /etc/profile.d/modules.sh
  +
module load gromacs
  +
export PATH=$PATH:/home/hpc/pr58ni/di34fol/masterprakt/task8/AGroS/
  +
AGroS 1a6zC.pdb -dir /home/hpc/pr58ni/di34fol/masterprakt/task8/models/1a6zC/ -threads 16 -v
  +
  +
<br style="clear:both;">

Latest revision as of 12:57, 2 July 2012

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


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