CD task8 protocol

From Bioinformatikpedia
Revision as of 14:44, 27 June 2012 by Vorbergs (talk | contribs) (Preparation)

Preparation

  • Load LRZ tools:
module load lrztools
  • Load git
module load git
  • clone git repository:
git clone git://github.com/offmarc/AGroS.git
  • SetPath
export PATH=$PATH:$HOME/AGroS/
  • Job script: job.sh
#!/bin/bash
#SBATCH -o /home/hpc/pr58ni/di34fog/jobs/wt/wt_md.out
#SBATCH -D /home/hpc/pr58ni/di34fog/jobs/wt
#SBATCH -J wt_MD
#SBATCH --partition=mpp1_inter
#SBATCH --get-user-env
#SBATCH --ntasks=32
#SBATCH --mail-type=end
#SBATCH --mail-user=susann.vorberg@cmapus.lmu.de
#SBATCH --export=NONE
#SBATCH --time=02:00:00
source /etc/profile.d/modules.sh
module load gromacs
export PATH="$HOME/AGroS:$PATH"
export PATH="$HOME/apps/bin/:$PATH"
export PATH="$HOME/software/scwrl/:$PATH"
AGroS 2O4H_chainA.pdb --scwrlPATH /home/hpc/pr58ni/di34fog/software/scwrl -dir /home/hpc/pr58ni/di34fog/jobs/wt -threads 32


  • Log in to:
ssh -X di34fog@lxia4-1
batch job.sh