autoimage（Automatically re-image coordinates 坐标自动重新成像）

Automatically center and image (by molecule) a trajectory with periodic boundaries. For most cases just specifying’autoimage’ alone is sufficient. The ’anchor’ molecule (default the first molecule) will be centered; all’fixed’ molecules will be imaged only if imaging brings them closer to the ’anchor’ molecule; default for ’fixed’molecules is all non-solvent non-ion molecules. All other molecules (referred to as ’mobile’) will be imaged freely. In general, the ’anchor’ molecule should be one that has the smallest distance to all ’fixed’ molecules.

"Fixed" : Molecules that should remain ’fixed’ to the anchor molecule; default is all non-ion/non-solvent molecules

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image（Re-image coordinates坐标自动重新成像）

Note this command is intended for advanced use; for most cases the autoimage command should be sufficient.

For periodic systems only, image molecules/residues/atoms that are outside of the box back into the box. Currently both orthorhombic and non-orthorhombic boxes are supported. A typical use of image is to move molecules back into the box after performing center. For example, the following commands move all atoms so that the center of residue 1 is at the center of the box, then image so that all molecules that are outside the box after centering are wrapped back inside:

center :1

image

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iwrap和unwrap

Under periodic boundary conditions, MD trajectories are not continuous if molecules are wrapped(imaged) into the central unit cell. Especially, in sander, with iwrap=1, molecular trajectories become discontinuous when a molecule crosses the boundary of the unit cell. This command, unwrap processes the trajectories to force the masked molecules continuous by translating the molecules into the neighboring unit cells. It is the opposite function of image, but this command can also be used to place molecules side by side, for example, two strands of a DNA duplex. However, this command fails when the masked molecules travel more than half of the box size within a single frame.

If the optional argument “reference” is specified, then the first frame is unwrapped according to the reference structure. Otherwise, the first frame is not modified. As an example, assume that :1-10 is the first strand of a DNA duplex and :11-20 is the other strand of the duplex. Then the following commands could be used to create system where the two strands are not separated artificially:

unwrap :1-20

center :1-20 mass origin

image origin center familiar