autoimage

Automatically re-image coordinates.

autoimage [<mask> | anchor <mask> [fixed <mask>] [mobile <mask>]][origin] [firstatom] [familiar | triclinic]

[<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.

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.