Morph is the command-line implementation of Morph Conformations; it creates a trajectory that morphs between two or more structures (see example systems). Each sequential pair of input structures serves as the starting and ending points of one segment of the trajectory, and a morph trajectory can have multiple segments. MD Movie is called to show the trajectory and can record it as a movie. Morphing is under development and has limitations.
The morph start command specifies the first structure (molecule model) in the trajectory and how to interpolate from that structure to the next. The entire molecule model containing the specified atoms will be used; atoms from more than one model should not be specified. A morph-name can be assigned with the name keyword, but is not necessary unless multiple morph trajectories will coexist. The default morph-name is default. All keywords to morph and their values except morph-name can be truncated to unambiguous strings.
The morph interpolate command specifies the next structure (molecule model) in the trajectory and how to interpolate from that structure to the one after it, if any. Since a morph trajectory can contain multiple segments, this command can be used multiple times for the same trajectory.
For both morph start and morph interpolate, additional options are:
| Option keyword | Possible values (see details) |
Defaults | |
|---|---|---|---|
| start | interpolate | ||
| method | corkscrew independent linear |
corkscrew | (same as preceding segment) |
| rate | linear "ramp down" "ramp up" sinusoidal |
linear | (same as preceding segment) |
| frames | (integers) | 20 | (same as preceding segment) |
| cartesian | true false |
false | false |
The morph movie command creates the trajectory and shows it using MD Movie. Whether to energy-minimize every interpolated conformation can be specified with minimize (default false, no minimization), and how many minimization steps to perform on each can be specified with step nsteps (default 60). Note that minimization has its own set of limitations and increases computational demands significantly.
The morph done command deletes the trajectory and exits from MD Movie.
See also: coordset, making movies