# vim:ft=plumed

# First load information about the molecule.
MOLINFO STRUCTURE=ref.pdb

# Define here the groups that you need
rna: GROUP ATOMS=1-258
mg:  GROUP ATOMS=6580
wat: GROUP ATOMS=259-6579

# Make RNA whole
WHOLEMOLECULES ENTITY0=rna

# Now make water whole as if it was a single molecule
WHOLEMOLECULES ENTITY0=wat

# And dump the resulting trajectory
DUMPATOMS ATOMS=rna,wat,mg FILE=wrong.gro
