autoimage

Automatically re-image coordinates.

autoimage [<mask> | anchor <mask> [fixed <mask>][mobile <mask>]]
          [origin] 
          [firstatom] 
          [{familiar | triclinic}]
          [moveanchor]
          [mode {bydist | byvec}]

[<mask> | anchor <mask>] Atoms to image around; this is the region that will be centered. Default is the entire first molecule.
[fixed <mask>] Molecules that should remain ’fixed’ to the anchor region; default is all non-ion/non-solvent molecules.
[mobile <mask>] Molecules that can be freely imaged; default is all ion/solvent molecules.
[origin] Center anchor region at the origin; if not specified, center at box center.
[firstatom] Image based on molecule first atom; default is to image by molecule center of mass.
[familiar] Image to familiar truncated-octahedral shape; this is on by default if the original cell is truncated octahedron.
[triclinic] Force general triclinic imaging.
[moveanchor] When treating “fixed” molecules, the anchor point will be set to the previous “fixed” molecule; this is only expected to work well when
“fixed” molecules that are sequential are also geometrically close. Most useful in more condensed systems like those containing membranes.
[mode {bydist|byvec}] How to treat “fixed” molecules.
bydist The default. “Fixed” molecules will use the image closest to the “anchor” molecule.
byvec “Fixed” molecules will use the image closest to their orientation with respect to the anchor in the first frame. May work better than ‘bydist’ for systems containing membranes.

Automatically center and image (by molecule) a trajectory with periodic boundaries. For most cases just specifying autoimage alone is sufficient. The atoms of the anchor region (default the entire 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.

The autoimage command works for the majority of systems; however, for very densely packed systems the default anchor (entire first molecule) may not be appropriate. In these cases, it is recommended to choose as the anchor a small region which should lie near the center of your system. For example, in a protein dimer system one could choose a single residue that is near the center of the interface between the two monomers. The ‘moveanchor‘ and ‘mode byvec‘ options may also help in cases where the system is more condensed, such as those containing membranes.