PBC

cpptraj <<EOF
parm ../ref.pdb reference ../ref.pdb [refx]
trajin ../${i}_trajout.xtc
autoimage
rms ref [refx] out rmsd-${i}.dat
trajout ${i}_autoimage_fit.xtc
trajout ${i}_look.pdb offset 1000
run
EOF

for loop 

for i in {0..25};do
cpptraj <<EOF
parm ../ref.pdb reference ../ref.pdb [refx]
trajin ../${i}_trajout.xtc
autoimage
rms ref [refx] out rmsd-${i}.dat
trajout ${i}_autoimage_fit.xtc
trajout ${i}_look.pdb offset 1000
run
EOF
done

cluster

#### sh cluster.sh
cpptraj <<EOF
parm ../com_first.pdb
trajin ../md_pbc_1.xtc 0 10000000
cluster C1 \
        hieragglo epsilon 5.0 linkage epsilonplot eposilonplot.dat \
        rms :1-330@C,N,O,CA,CB&!@H= \
        sieve 10 random \
    out cnumvtime.dat \
        sil Sil \
        summary summary.dat \
        info info.dat \
        cpopvtime cpopvtime.agr normframe \
        repout rep repfmt pdb \
        singlerepout singlerep.nc singlerepfmt netcdf \
        avgout Avg avgfmt pdb
run
EOF