Have run a simulation with AMBER and want to continue with NAMD? That's what you need:
perl amber2namd.pl amber_topology_file amber_restart_file root_namd_files
It creates a NAMD configuration file with all the needed periodic boundary definitions (assumes for truncated octahedron) + a velocities PDB file (needs ambpdb) to do a proper restart.
1) there may be some difference in the kinetic energy due to the 3 decimals limit in the velocities PDB file
2) the vdw energies will not be identical because for periodic systems AMBER introduces a correction term for the van der Waals that is a function of preassure and energy (vdwmeth=1), while NAMD does not. See this link for further details:
If you want to run metadynamics with NAMD, all you have to do is:
1) include these lines in your MD configuration file:
colvarsConfig colvars_dihedral.conf # colective variable configuration file
#colvarsInput meta_3.restart.colvars.state # COMMENT OUT UNLEES YOU RESTART A JOB
2) Create a colvars configuration file.
This is an example for distance constraint: