Bash tips

Read a number from a file

number=$( awk '{print $0}' number.dat )

Interact with the GROMACS prompt

gmx trjconv -f prod.xtc -s prod.tpr -o prod.mol.xtc -pbc mol<<EOF
    0
EOF

For loop

for i in {1..5}
do
  true
done

Read file

while IFS= read -r line
do
    echo "$line"
done < file.txt

Read end of a string

string="blabla"
sub-string=${string:3:0-1}${string:0-1}

Interact with LAMMPS variable

mpirun -np 16 lmp_mpi -in input.lammps -var f 0.01

Replace in a file

newline='variable  = '$a  
oldline=$(cat myfile| grep 'variable  = ')  
sed -i '/'"$oldline"'/c\'"$newline" myfile