To enable PLUMED in a NAMD simulation one should add the following lines in the NAMD configuration file (often named as xxx.namd or xxx.conf) and run the plumed-patched version of NAMD with it:
plumed on plumedfile plumed.dat
The first line tells NAMD to run with PLUMED and the second line specifies the PLUMED input file.
For more information on NAMD you should visit http://www.ks.uiuc.edu/Research/namd/