Task 10 - Journal (PKU)

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<<EOF0\nEOF

1. center protein in the box

trjconv -f _traj_nojump.xtc -s _solv.pdb -center -o _traj_center.xtc<<EOF1\n0\nEOF

1. eliminate rotations

trjconv -f _traj_center.xtc -s _solv.pdb -fit rot+trans -o _norot.xtc<<EOF1\n0\nEOF

1. create pdb file

trjconv -f _norot.xtc -s _solv.pdb -o _traj.pdb<<EOF1\nEOF

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<<EOF1\nEOF

</source>