Difference between revisions of "Molecular Dynamics Simulations Gaucher Disease Scripts"

From Bioinformatikpedia
(Created page with "== Wildtype == <pre> #!/bin/bash #SBATCH -o /home/hpc/pr58ni/di34fon/mp/tasks/task08/2nt0_A_L470P/out #!/bin/bash #SBATCH -o /home/hpc/pr58ni/di34fon/mp/tasks/task08/2nt0_A_W209R…")
 
 
Line 2: Line 2:
 
<pre>
  
<pre>
 
#!/bin/bash
  
#!/bin/bash
−
#SBATCH -o /home/hpc/pr58ni/di34fon/mp/tasks/task08/2nt0_A_L470P/out
 +
#SBATCH -o /home/hpc/pr58ni/di34fon/mp/tasks/task08/2nt0_A/long/out
  +
#SBATCH -D /home/hpc/pr58ni/di34fon/mp/tasks/task08/2nt0_A/long/
−
#!/bin/bash
  
−
#SBATCH -o /home/hpc/pr58ni/di34fon/mp/tasks/task08/2nt0_A_W209R/out
  
−
#!/bin/bash
  
−
#SBATCH -o /home/hpc/pr58ni/di34fon/mp/tasks/task08/2nt0_A/out
  
−
#SBATCH -D /home/hpc/pr58ni/di34fon/mp/tasks/task08/2nt0_A/
  
 
#SBATCH -J 2nt0_A
 
#SBATCH -J 2nt0_A
−
#SBATCH --partition=mpp1_inter
 +
#SBATCH --clusters=mpp1
 
#SBATCH --get-user-env
  
#SBATCH --get-user-env
−
#SBATCH --ntasks=32
 +
#SBATCH --ntasks=16
 
#SBATCH --mail-type=end
  
#SBATCH --mail-type=end
−
#SBATCH --mail-user=offman@lrz.de
 +
#SBATCH --mail-user=angermue@in.tum.de
 
#SBATCH --export=NONE
  
#SBATCH --export=NONE
−
#SBATCH --time=02:00:00
 +
#SBATCH --time=32:00:00
 
source /etc/profile.d/modules.sh
  
source /etc/profile.d/modules.sh
 
module load gromacs
  
module load gromacs
 
ROOT=/home/hpc/pr58ni/di34fon/mp/tasks/task08
  
ROOT=/home/hpc/pr58ni/di34fon/mp/tasks/task08
 
export PATH="$ROOT/ag:$PATH"
  
export PATH="$ROOT/ag:$PATH"
−
AGroS 2nt0_A.pdb -dir $ROOT/2nt0_A -threads 32
 +
AGroS 2nt0_A.pdb -dir $ROOT/2nt0_A/long -threads 16 -v
 
</pre>
  
</pre>
   
Line 26: Line 22:
 
<pre>
  
<pre>
 
#!/bin/bash
  
#!/bin/bash
−
#SBATCH -o /home/hpc/pr58ni/di34fon/mp/tasks/task08/2nt0_A_W209R/out
 +
#SBATCH -o /home/hpc/pr58ni/di34fon/mp/tasks/task08/2nt0_A_W209R/long/out
−
#SBATCH -D /home/hpc/pr58ni/di34fon/mp/tasks/task08/2nt0_A_W209R/
 +
#SBATCH -D /home/hpc/pr58ni/di34fon/mp/tasks/task08/2nt0_A_W209R/long/
 
#SBATCH -J 2nt0_A_W209R
  
#SBATCH -J 2nt0_A_W209R
−
#SBATCH --partition=mpp1_inter
 +
#SBATCH --clusters=mpp1
 
#SBATCH --get-user-env
  
#SBATCH --get-user-env
 
#SBATCH --ntasks=32
  
#SBATCH --ntasks=32
 
#SBATCH --mail-type=end
  
#SBATCH --mail-type=end
−
#SBATCH --mail-user=offman@lrz.de
 +
#SBATCH --mail-user=angermue@in.tum.de
 
#SBATCH --export=NONE
  
#SBATCH --export=NONE
−
#SBATCH --time=02:00:00
 +
#SBATCH --time=32:00:00
 
source /etc/profile.d/modules.sh
  
source /etc/profile.d/modules.sh
 
module load gromacs
  
module load gromacs
 
ROOT=/home/hpc/pr58ni/di34fon/mp/tasks/task08
  
ROOT=/home/hpc/pr58ni/di34fon/mp/tasks/task08
 
export PATH="$ROOT/ag:$PATH"
  
export PATH="$ROOT/ag:$PATH"
−
AGroS 2nt0_A_W209R.pdb -dir $ROOT/2nt0_A_W209R -threads 32
 +
AGroS 2nt0_A_W209R.pdb -dir $ROOT/2nt0_A_W209R/long -threads 32
 
</pre>
  
</pre>
   
Line 46: Line 42:
 
<pre>
  
<pre>
 
#!/bin/bash
  
#!/bin/bash
−
#SBATCH -o /home/hpc/pr58ni/di34fon/mp/tasks/task08/2nt0_A_L470P/out
 +
#SBATCH -o /home/hpc/pr58ni/di34fon/mp/tasks/task08/2nt0_A_L470P/long/out
−
#SBATCH -D /home/hpc/pr58ni/di34fon/mp/tasks/task08/2nt0_A_L470P/
 +
#SBATCH -D /home/hpc/pr58ni/di34fon/mp/tasks/task08/2nt0_A_L470P/long/
 
#SBATCH -J 2nt0_A_L470P
 
#SBATCH -J 2nt0_A_L470P
−
#SBATCH --partition=mpp1_inter
 +
#SBATCH --clusters=mpp1
 
#SBATCH --get-user-env
  
#SBATCH --get-user-env
 
#SBATCH --ntasks=32
  
#SBATCH --ntasks=32
 
#SBATCH --mail-type=end
  
#SBATCH --mail-type=end
−
#SBATCH --mail-user=offman@lrz.de
 +
#SBATCH --mail-user=angermue@in.tum.de
 
#SBATCH --export=NONE
  
#SBATCH --export=NONE
−
#SBATCH --time=02:00:00
 +
#SBATCH --time=32:00:00
 
source /etc/profile.d/modules.sh
  
source /etc/profile.d/modules.sh
 
module load gromacs
  
module load gromacs
 
ROOT=/home/hpc/pr58ni/di34fon/mp/tasks/task08
  
ROOT=/home/hpc/pr58ni/di34fon/mp/tasks/task08
 
export PATH="$ROOT/ag:$PATH"
  
export PATH="$ROOT/ag:$PATH"
−
AGroS 2nt0_A_L470P.pdb -dir $ROOT/2nt0_A_L470P -threads 32
 +
AGroS 2nt0_A_L470P.pdb -dir $ROOT/2nt0_A_L470P/long -threads 32
 
</pre>
  
</pre>

Latest revision as of 15:57, 28 June 2012

Wildtype

#!/bin/bash
#SBATCH -o /home/hpc/pr58ni/di34fon/mp/tasks/task08/2nt0_A/long/out
#SBATCH -D /home/hpc/pr58ni/di34fon/mp/tasks/task08/2nt0_A/long/
#SBATCH -J 2nt0_A 
#SBATCH --clusters=mpp1
#SBATCH --get-user-env
#SBATCH --ntasks=16
#SBATCH --mail-type=end
#SBATCH --mail-user=angermue@in.tum.de
#SBATCH --export=NONE
#SBATCH --time=32:00:00
source /etc/profile.d/modules.sh
module load gromacs
ROOT=/home/hpc/pr58ni/di34fon/mp/tasks/task08
export PATH="$ROOT/ag:$PATH"
AGroS 2nt0_A.pdb -dir $ROOT/2nt0_A/long -threads 16 -v

W209R

#!/bin/bash
#SBATCH -o /home/hpc/pr58ni/di34fon/mp/tasks/task08/2nt0_A_W209R/long/out
#SBATCH -D /home/hpc/pr58ni/di34fon/mp/tasks/task08/2nt0_A_W209R/long/
#SBATCH -J 2nt0_A_W209R
#SBATCH --clusters=mpp1
#SBATCH --get-user-env
#SBATCH --ntasks=32
#SBATCH --mail-type=end
#SBATCH --mail-user=angermue@in.tum.de
#SBATCH --export=NONE
#SBATCH --time=32:00:00
source /etc/profile.d/modules.sh
module load gromacs
ROOT=/home/hpc/pr58ni/di34fon/mp/tasks/task08
export PATH="$ROOT/ag:$PATH"
AGroS 2nt0_A_W209R.pdb -dir $ROOT/2nt0_A_W209R/long -threads 32

L470P

#!/bin/bash
#SBATCH -o /home/hpc/pr58ni/di34fon/mp/tasks/task08/2nt0_A_L470P/long/out
#SBATCH -D /home/hpc/pr58ni/di34fon/mp/tasks/task08/2nt0_A_L470P/long/
#SBATCH -J 2nt0_A_L470P 
#SBATCH --clusters=mpp1
#SBATCH --get-user-env
#SBATCH --ntasks=32
#SBATCH --mail-type=end
#SBATCH --mail-user=angermue@in.tum.de
#SBATCH --export=NONE
#SBATCH --time=32:00:00
source /etc/profile.d/modules.sh
module load gromacs
ROOT=/home/hpc/pr58ni/di34fon/mp/tasks/task08
export PATH="$ROOT/ag:$PATH"
AGroS 2nt0_A_L470P.pdb -dir $ROOT/2nt0_A_L470P/long -threads 32
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