Difference between revisions of "Task 10 - Journal (PKU)"
From Bioinformatikpedia
(→create trajectories) |
(→create trajectories) |
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Line 22: | Line 22: | ||
trjconv -f _norot.xtc -s _solv.pdb -o _traj.pdb<<EOF1\nEOF |
trjconv -f _norot.xtc -s _solv.pdb -o _traj.pdb<<EOF1\nEOF |
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#reduce fluctuations and write every fifth frame |
#reduce fluctuations and write every fifth frame |
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− | g_filter -f _traj.pdb -s |
+ | g_filter -f _traj.pdb -s _solv.pdb -ol _traj_filtered.pdb -fit -nf 5<<EOF1\nEOF |
</source> |
</source> |
Revision as of 12:12, 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<<EOF0\nEOF
- center protein in the box
trjconv -f _traj_nojump.xtc -s _solv.pdb -center -o _traj_center.xtc<<EOF1\n0\nEOF
- eliminate rotations
trjconv -f _traj_center.xtc -s _solv.pdb -fit rot+trans -o _norot.xtc<<EOF1\n0\nEOF
- create pdb file
trjconv -f _norot.xtc -s _solv.pdb -o _traj.pdb<<EOF1\nEOF
- reduce fluctuations and write every fifth frame
g_filter -f _traj.pdb -s _solv.pdb -ol _traj_filtered.pdb -fit -nf 5<<EOF1\nEOF
</source>