Cluster only non-hydrogen atoms atoms
#make index file with non-hydrogen atoms, use 1 & ! a H* and q for input !{gromacs_s} **-i q **-- make_ndx -f md/md1.tpr -o mtd/index.ndx #include index file and select index group 3 !{gromacs_s} -i {groups} -- cluster -method gromos -f mtd/mtd1.trr -s mtd/w0/mtd1.tpr -n index.ndx -cutoff 0.15 -cl clustering/outCluster.pdb