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>")
 
(Initial checks)
Line 3: Line 3:
 
<source lang="bash">
 
<source lang="bash">
 
gmxcheck -f _md.xtc
 
gmxcheck -f _md.xtc
  +
</source>
  +
  +
performance statistics:
  +
<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
  +
 
</source>
 
</source>

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">

  1. fix jumps over the periodic boundary

trjconv -f _md.xtc -s _solv.pdb -pbc nojump -o _traj_nojump.xtc

  1. center protein in the box

trjconv -f _traj_nojump.xtc -s _solv.pdb -center -o _traj_center.xtc

  1. eliminate rotations

trjconv -f _traj_center.xtc -s _solv.pdb -fit rot+trans -o _norot.xtc

  1. create pdb file

trjconv -f _norot.xtc -s _solv.pdb -o _traj.pdb

  1. 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>