Difference between revisions of "Fabry:Molecular Dynamics Simulations/Journal"
From Bioinformatikpedia
Rackersederj (talk | contribs) |
Rackersederj (talk | contribs) |
||
| Line 1: | Line 1: | ||
| − | [[Fabry Disease]] » [[Fabry:Molecular_Dynamics_Simulations | Molecular Dynamics Simulations]] » Journal |
+ | [[File:Example.jpg]][[Fabry Disease]] » [[Fabry:Molecular_Dynamics_Simulations | Molecular Dynamics Simulations]] » Journal |
<hr> |
<hr> |
||
[[Category: Fabry Disease 2012]] |
[[Category: Fabry Disease 2012]] |
||
| Line 16: | Line 16: | ||
sbatch jobs/XXX_real.script |
sbatch jobs/XXX_real.script |
||
squeue -u di34fat --cluster=mpp1 |
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 |
||
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
