Difference between revisions of "Fabry:Molecular Dynamics Simulations/Journal"

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sbatch WT.script
 
sbatch WT.script
 
squeue -u di34fat --partition=mpp1_inter > job
  
squeue -u di34fat --partition=mpp1_inter > job
  +
  +
sbatch jobs/XXX_real.script
  +
squeue -u di34fat --cluster=mpp1
  +
  +
=== Trajectory ===
  +
  +
Create the trajectory file ([[Molecular_Dynamics_Simulations_(PKU) | thanks to PKU!!!]])
  +
trjconv -s 3S5Y_chainA_repaired_solv_min3.tpr -f 3S5Y_chainA_repaired_md.xtc -o traj_wt.pdb -dt 10
  +
  +
Each frame of the trajectory file can be converted into a png with pymol
  +
set ray_trace_frames, 1
  +
mpng movie
  +
  +
The pngs were merged to an animated gif
  +
convert *.png ani.gif

Latest revision as of 14:53, 2 July 2012

Fabry Disease » Molecular Dynamics Simulations  » Journal 

module load git
git clone git://github.com/offmarc/AGroS.git
export PATH=$PATH:$HOME/AGroS/

export PATH=$PATH:/home/hpc/pr58ni/di34fat/AGroS/./../software/scwrl4
mv ~/software/scwrl4/Scwrl4 ~/software/scwrl4/scwrl
ssh -X lxia4-1
cd AGroS/
sbatch WT.script 
squeue -u di34fat --partition=mpp1_inter > job

sbatch jobs/XXX_real.script
squeue -u di34fat --cluster=mpp1

Trajectory

Create the trajectory file ( thanks to PKU!!!) 

trjconv -s 3S5Y_chainA_repaired_solv_min3.tpr -f 3S5Y_chainA_repaired_md.xtc -o traj_wt.pdb -dt 10

Each frame of the trajectory file can be converted into a png with pymol 

set ray_trace_frames, 1
mpng movie

The pngs were merged to an animated gif 

convert *.png ani.gif
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