# 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

# Here's a compund variable with the box vectors
# computed before aligning RNA
cell_before: CELL

# Now we align RNA
FIT_TO_TEMPLATE REFERENCE=ref-rna.pdb TYPE=OPTIMAL

# Here's a compund variable with the box vectors
# computed after aligning RNA
cell_after: CELL
PRINT ARG=cell_before.* FILE=CELL_BEFORE
PRINT ARG=cell_after.* FILE=CELL_AFTER
