Moving Constraints

Moving constraints feature works in conjunction with the Harmonic Constraints (see an appropriate section of the User's guide). The reference positions of all constraints will move according to

$$\vec r(t) \; = \; \vec r_0 \, + \, \vec v t \,.$$ (30)

A velocity vector $\vec v$ (movingConsVel) needs to be specified.

The way the moving constraints work is that the moving reference position is calculated every integration time step using Eq. 30, where $\vec v$ is in Å/timestep, and $t$ is the current timestep (i.e., firstTimestep plus however many timesteps have passed since the beginning of NAMD run). Therefore, one should be careful when restarting simulations to appropriately update the firstTimestep parameter in the NAMD configuration file or the reference position specified in the reference PDB file.

NOTE: NAMD actually calculates the constraints potential with $U = k (x-x_0)^d$ and the force with $F = d k (x-x_0)$ , where $d$ is the exponent consexp. The result is that if one specifies some value for the force constant $k$ in the PDB file, effectively, the force constant is $2 k$ in calculations. This caveat was removed in SMD feature.

The following parameters describe the parameters for the moving harmonic constraint feature of NAMD.

• movingConstraints $<$ Are moving constraints active $>$
  Acceptable Values: on or off
  Default Value: off
  Description: Should moving restraints be applied to the system. If set to on, then movingConsVel must be defined. May not be used with rotConstraints.

• movingConsVel $<$ Velocity of the reference position movement $>$
  Acceptable Values: vector in Å/timestep
  Description: The velocity of the reference position movement. Gives both absolute value and direction