Added an example

# Solvated 5-mer peptide

units		real

atom_style	full

pair_style	lj/charmm/coul/long 8.0 10.0 10.0

bond_style      harmonic

angle_style     charmm

dihedral_style  charmm

improper_style  harmonic

kspace_style	pppm 0.0001

read_data	data.peptide

neighbor	2.0 bin

neigh_modify	delay 5

timestep	2.0

group		peptide type <= 12

group		one id 2 4 5 6

group		two id 80 82 83 84

group		ref id 37

group		colvar union one two ref

fix		1 all nvt temp  275.0 275.0 100.0 tchain 1

fix		2 all plumed plumedfile plumed.dat outfile p.log

fix		2a ref setforce 0.0 0.0 0.0

fix		4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31

#dump		1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz

#dump_modify 1 sort id

thermo_style	custom step temp etotal pe ke epair ebond f_2

thermo		10

run		100

c1: COM ATOMS=2,4,5,6

c2: COM ATOMS=80,82,83,84

d1: DISTANCE ATOMS=c1,37

d2: DISTANCE ATOMS=c2,37

h_pot: RESTRAINT ARG=d1,d2 CENTER=1.0,1.0 KAPPA=10,10

PRINT ARG=d1,d2,h_pot.*