The SMD feature is independent from the harmonic constraints, although it follows the same ideas. In both SMD and harmonic constraints, one specifies a PDB file which indicates which atoms are 'tagged' as constrained. The PDB file also gives initial coordinates for the constraint positions. One also specifies such parameters as the force constant(s) for the constraints, and the velocity with which the constraints move.
There are two major differences between SMD and harmonic constraints:
The center of mass of the SMD atoms will be harmonically constrained with force constant (SMDk) to move with velocity (SMDVel) in the direction (SMDDir). SMD thus results in the following potential being applied to the system:
Optionally, one may also specify a transverse force constant (SMDk2). The potential then becomes
NAMD provides output of the current SMD data. The frequency of output is specified by the SMDOutputFreq parameter in the configuration file. Every SMDOutputFreq timesteps NAMD will print the current timestep, current position of the center of mass of the restrained atoms, and the current force applied to the center of mass (in piconewtons, pN). The output line starts with word SMD
The following parameters describe the parameters for the SMD feature of NAMD.