Minimization

NAMD provides a simple form of a depth first search to perform energy minimization. This method uses a modified form of the Verlet method described above. It is modified in two ways. The first is that the velocity of the particles is set to zero after each timestep. This means that direction of movement of each particle during an integration step will always be in the direction of the gradient, thus createing a depth first serach. The second modification is to place a bound on the movement of an atom during any timestep, since a structure with very high potential energies may experience very rapid movement of atoms during the beginning of minimization. The amount of movement per timestep can be specified using the configuration option maximumMove. If no value is specified, NAMD will assume a default value of

$$\frac{0.75 \times \texttt{pairlistDistr}}{\texttt{stepsPerCycle}},$$

where the parameter pairlistDist is the bounding distance between pairs for inclusion in pairlists, and the parameter stepsPerCycle indicates the number of time steps between pairlist generation. See section 4 for more details about these configuration parameters. The default value for maximumMove insures that no atom can move more than 3/4 of the pairlist distance during a cycle. If greater accuracy in the energy calculation is desired, then this value should be reduced.