Fabry:Molecular Dynamics Simulations/Journal

Fabry Disease » Molecular Dynamics Simulations  » Journal

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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