View source for Task8 Hemochromatosis Protocol

== Getting started ==


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=== 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/

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=== Setting up SCWRL4 ===


Install SCWRL4 into AGroS directory.
Add link from "scwrl" to "Scwrl4" (otherwise AGroS won't find it).
 ln -s Scwrl4 scwrl


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=== 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!

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== 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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