Gaucher Task10 Protocol

Sources

You can checkout the git repository containing all relevant data an scripts by:

git clone /mnt/home/student/angermue/mp/tasks/task10

Checking the results

gmxcheck -f traj.xtc 

Visualizing the results

Given the reference structure $REF, we corrected the trajectory file $TRAJ.xtc as follows:

trjconv -f $TRAJ.xtc -s $REF -pbc nojump -o ${TRAJ}_nojump.xtc <<EOF
0
EOF
trjconv -f ${TRAJ}_nojump.xtc -s $REF -center -o ${TRAJ}_center.xtc <<EOF
1
0
EOF
trjconv -f ${TRAJ}_center.xtc -s $REF -fit rot+trans -o ${TRAJ}_norot.xtc <<EOF
1
0
EOF

Next, we created a PDB file with several states using the time resolution $TIME=10:

trjconv -f ${TRAJ}_norot.xtc -s $REF -o ${TRAJ}_traj.pdb <<EOF
1
EOF
g_filter -f ${TRAJ}_traj.pdb -s $REF -ol ${TRAJ}_traj_$TIME.pdb -fit -nf $TIME <<EOF
1
EOF