echo extracting some configurations
gmx trjconv -f traj.trr -o sample.trr -b 100 -dt 100 -pbc whole
echo extracting a pdb file needed by sassena
gmx trjconv -f traj.trr -o sample.pdb -b 1900 -dt 100 -pbc whole -sep
echo changing the name of pdb file
mv sample0.pdb sample.pdb
echo translating from trr to dcd
catdcd -o sample.dcd -trr sample.trr
echo running sassena
sassena
echo extracting qvectors
ncdump signal.h5 -v qvectors > qvectors.txt
echo extracting fq
ncdump signal.h5 -v fq > fq.txt
echo merging qvectors with signal
paste qvectors.txt fq.txt > fq.dat
echo deleting the first 24 lines
cat fq.dat | tail -n +24 > fq_NH.dat