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.

Bug: NAMD does not currently take into account virial contributions from PLUMED. Please use constant volume simulations only.

For more information on NAMD you should visit http://www.ks.uiuc.edu/Research/namd/