View source for Fabry:Molecular Dynamics Simulations/Journal

[[Fabry Disease]] » [[Fabry:Molecular_Dynamics_Simulations | Molecular Dynamics Simulations]]  » Journal
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[[Category: Fabry Disease 2012]]

 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 ([[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