Moving constraints

Moving constraints allow NAMD to run steered molecular dynamics (SMD) simulations. This feature is based on the harmonic constraints feature, and effectively allows for the reference position of a specified atom to move with a constant velocity $\vec v$. The potential for this atom is computed according to

$$E_{\text{smd}}(t) \; = \; k_i \, \left( \vert\vec r_{\text{ref}}(t) \, - \, \vec r_i(t)\vert \right)^e$$

where

• t = time
• ${\vec{r}}_i$ = position of atom i
• $\vec r_{\text{ref}}(t) = \vec r(0) + \vec v t$, current reference position (position of the restraint point)
• e = exponent defined for all constraints

In addition to the usual harmonic constraint parameters, the constant velocity vector $\vec v$ must be specified by parameter movingConsVel, and the index of the constrained atom (using 0-based indexing) must be specified by parameter movingConsAtom. See section 4.

The way the moving constraints work is that the moving reference position is calculated every integration time step with $\vec v$ in Å/timestep and t 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 either the firstTimestep parameter in the NAMD configuration file or the reference position specified in the reference PDB file.