Difference between revisions of "Task 10 - Journal (PKU)"
From Bioinformatikpedia
(Created page with "== Initial checks == Verify completion, frame number and frame rate: <source lang="bash"> gmxcheck -f _md.xtc </source>") |
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<source lang="bash"> |
<source lang="bash"> |
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gmxcheck -f _md.xtc |
gmxcheck -f _md.xtc |
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| + | </source> |
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| + | |||
| + | performance statistics: |
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| + | <source lang="bash"> |
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| + | tail _md.log |
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| + | </source> |
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| + | |||
| + | ==create trajectories== |
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| + | |||
| + | <source lang="bash"> |
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| + | #fix jumps over the periodic boundary |
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| + | trjconv -f _md.xtc -s _solv.pdb -pbc nojump -o _traj_nojump.xtc |
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| + | #center protein in the box |
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| + | trjconv -f _traj_nojump.xtc -s _solv.pdb -center -o _traj_center.xtc |
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| + | #eliminate rotations |
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| + | trjconv -f _traj_center.xtc -s _solv.pdb -fit rot+trans -o _norot.xtc |
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| + | #create pdb file |
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| + | trjconv -f _norot.xtc -s _solv.pdb -o _traj.pdb |
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| + | #reduce fluctuations and write every fifth frame |
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| + | g_filter -f 1J8U_traj.pdb -s 1J8U_solv.pdb -ol _traj_filtered.pdb -fit -nf 5 |
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| + | |||
</source> |
</source> |
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Revision as of 12:06, 11 July 2012
Initial checks
Verify completion, frame number and frame rate: <source lang="bash"> gmxcheck -f _md.xtc </source>
performance statistics: <source lang="bash"> tail _md.log </source>
create trajectories
<source lang="bash">
- fix jumps over the periodic boundary
trjconv -f _md.xtc -s _solv.pdb -pbc nojump -o _traj_nojump.xtc
- center protein in the box
trjconv -f _traj_nojump.xtc -s _solv.pdb -center -o _traj_center.xtc
- eliminate rotations
trjconv -f _traj_center.xtc -s _solv.pdb -fit rot+trans -o _norot.xtc
- create pdb file
trjconv -f _norot.xtc -s _solv.pdb -o _traj.pdb
- reduce fluctuations and write every fifth frame
g_filter -f 1J8U_traj.pdb -s 1J8U_solv.pdb -ol _traj_filtered.pdb -fit -nf 5
</source>
