unwrap

Reverse of image; unwrap selected atoms so they have continuous trajectories.

unwrap [center] [{bymol | byres | byatom}] [ reference | ref <name> | refindex <#> ] [<mask>]

[center] Unwrap by center of mass; otherwise unwrap by first atom position.
bymol Unwrap by molecule (default).
byres Unwrap by residue.
byatom Unwrap by atom.
[ reference | ref <name> | refindex <#> ] Reference structure to use in unwrapping.
[<mask>] Selection to 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