Load a single trajectory frame as a reference.
reference <name> [<frame#>] [<mask>] ([tag]) [lastframe] [crdset][parm <parmfile / tag> | parmindex <#>]
<name> File name (or COORDS set name if ’crdset’ specified) to read in as reference; any trajectory recognized by ’trajin’ can be used.
[<frame#>] Frame number to use (default 1).
[<mask>] Only load atoms corresponding to <mask> from reference.
([tag]) Tag to give this reference file, e.g. “[MyRef]”; BRACKETS MUST BE INCLUDED.
[lastframe] Use last frame of reference.
[crdset] Use for COORDS data set named <name> instead of file.
[parm <parmfile/tag>] Topology filename/tag to associate with reference (default first topology).
[parmindex <#>] Index of Topology to associate with reference (default 0, first topology).
Use specified trajectory as reference coordinates. For trajectories with multiple frames, the first frame is used if a specific frame is not specified. An optional tag can be given (bounded in brackets) which can then be used in place of the name (follow this link for examples of how to use tags). If desired, an atom mask can be used to read in only specified atoms from a reference.
Reference coordinates are now considered COORDS data sets and can be used anywhere a COORDS data set could, which allows reference structures to be manipulated once they are loaded. For example, a reference structure could be centered on the origin like so:
reference tz2.rst7 [MyRef] crdaction [MyRef] center origin
Note that the ’average’ keyword has been deprecated for reference. If desired, an averaged reference COORDS data set can be created from a trajectory using the ’average’ command like so:
parm myparm.parm7 trajin mytraj.nc rms first :1-12 average crdset RefAvg run rms ToAvg reference :1-12 out ToAvg.dat