drms | drmsd (distance RMSD)
Calculate the RMSD of distance pairs within selected atoms.
drmsd [<dataset name>] [<mask> [<refmask>]] [out <filename>] [ first | ref <refname> | refindex <#> | reftraj <trajname> [parm <trajparm> | parmindex <parm#>] ]
[<dataset name>] Output data set name.
[<mask>] Atoms to calculate DRMSD for.
[<refmask>] Mask corresponding to atoms in reference; if not specified, <mask> is used.
[out <filename>] Output file name.
[first] Use the first trajectory frame processed as reference.
[reference] Use the first previously read in reference structure.
[ref <refname>] Use previously read in reference structure specified by <refname>.
[refindex <#>] Use previously read in reference structure specified by <#> (based on order read in).
previous Use frame prior to current frame as reference.
reftraj <name> Use frames from COORDS set <name> or read in from trajectory file <name> as references. Each frame from <name> is used in turn, so that frame 1 is compared to frame 1 from <name>, frame 2 is compared to frame 2 from <name> and so on. If <trajname> runs out of frames before processing is complete, the last frame of <trajname> continues to be used as the reference.
parm <parmname> | parmindex <#> If reftraj specifies a file associate trajectory <name> with specified topology; if not specified the first topology is used.
Calculate the distance RMSD (i.e. the RMSD of all pairs of internal distances) between atoms in the frame defined by <mask> (all if no <mask> specified) to atoms in a reference defined by <refmask> (<mask> if <refmask> not specified). Both <mask> and <refmask> must specify the same number of atoms, otherwise an error will occur.
Because this method compares pairs of internal distances and not absolute coordinates, it is not sensitive to translations and rotations the way that a no-fit RMSD calculation is. It can be more time consuming however, as 
For example, to get the DRMSD of a residue named LIG to its structure in the first frame read in:
drmsd :LIG first out drmsd.dat