Task 8 - Jorunal (PKU)

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Job submission

The following script was used to submit AGroS to the queue. For the two mutants this worked flawlessly, the wildtype required a bit more work. <source lang="bash">

#SBATCH -o $HOME/logs/<NAME>_MD.out
#SBATCH -J 1J8U_wildtype
#SBATCH --clusters=mpp1
#SBATCH --get-user-env
#SBATCH --ntasks=32
#SBATCH --mail-type=end
#SBATCH --mail-user=<email>
#SBATCH --export=NONE
#SBATCH --time=10:00:00
source /etc/profile.d/modules.sh
module load gromacs

cd $HOME/MD/
$HOME/AGroS/AGroS $HOME/Gromacs/Models/*.pdb -dir $HOME/MD/ -threads 32 --scwrlPATH $HOME/SCWRL

</source> Since the wildtype repeatedly had problems equilibrating and minimizing and broke the script several times, we took the intermediate results of AGroS after a breakdown, checked 1J8U_solv_min.pdb briefly for errors and called the next preparation steps of AGroS by hand: <source lang="bash">

repairPDB 1J8U_solv_min.pdb -jprot > 1J8U_solv_min.pdb2
genrestr -f 1J8U_solv_min_0.pdb -o posre.itp
grompp -v -f minim_solv.mdp -c 1J8U_solv_min.pdb -p 1J8U_solv.top -o 1J8U_solv_min2.tpr
mdrun -v -deffnm 1J8U_solv_min2.tpr -c 1J8U_solv_min2.pdb

#create minim_solv2.mdp according to AGroS
grompp -v -f minim_solv2.mdp -c 1J8U_solv_min2.pdb -p 1J8U_solv.top -o 1J8U_solv_min3.tpr
mdrun -v -deffnm 1J8U_solv_min3.tpr -c 1J8U_solv_min3.pdb

#create nvt.mdp according to AGroS
grompp -v -f nvt.mdp -c 1J8U_solv_min3.pdb -p 1J8U_solv.top -o 1J8U_nvt.tpr
mdrun -v -deffnm 1J8U_nvt

#create npt.mdp according to AGroS
grompp -v -f npt.mdp -c 1J8U_nvt.gro -p 1J8U_solv.top -o 1J8U_npt.tpr
mdrun -v -deffnm 1J8U_npt

#create md.mdp according to AGroS
grompp -v -f md.mdp -c 1J8U_npt.gro -p 1J8U_solv.top -o 1J8U_md.tpr

</source> The final run was submited to the queue with the following script:

<source lang="bash">

  1. !/bin/bash
  2. SBATCH -o $HOME/logs/1J8U_wildtype_MD.out
  3. SBATCH -D $HOME/testrun/
  4. SBATCH -J 1J8U_wildtype
  5. SBATCH --clusters=mpp1
  6. SBATCH --get-user-env
  7. SBATCH --ntasks=32
  8. SBATCH --mail-type=end
  9. SBATCH --mail-user=<email>
  10. SBATCH --export=NONE
  11. SBATCH --time=10:00:00

source /etc/profile.d/modules.sh module load gromacs export PATH="$HOME/AGroS:$PATH" cd $HOME mpiexec -n 32 mdrun_mpi -v -deffnm $HOME/MD/mdrun_1J8U/1J8U_md </source>