Perform best fit of coordinates to reference and calculate coordinate RMSD.

rmsd [<name>] <mask> [<refmask>] [out filename] [nofit | norotate | nomod] [mass] [savematrices] [ first | reference | ref <name> | refindex <#> | previous | reftraj <name> [parm <name> | parmindex <#>] ] [perres perresout <filename> [perresavg <avgfile>] [range <resRange>] [refrange <refRange>] [perresmask <additional mask>] [perrescenter] [perresinvert]

[<name>] Output data set name.
[<mask>] Mask of atoms to calculate RMSD for; if not specified, calculate for all atoms.
[<refmask>] Reference mask; if not specified, use <mask>.
[out <filename>] Output data file name.
[nofit] Do not perform best-fit RMSD.
[norotate] If calculating best-fit RMSD, translate but do not rotate coordinates.
[nomod] If calculating best-fit RMSD, do not modify coordinates.
[mass] Mass-weight the RMSD calculation.
[savematrices] If specified save rotation matrices to data set with aspect [RM].

Reference keywords:
first Use the first trajectory frame processed as reference.
reference Use the first previously read in reference structure (refindex 0).
ref <name> Use previously read in reference structure specified by filename/tag.
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 trajectory file, associate it with specified topology; if not specified the first topology is used.

Per-residue RMSD keywords:
perres Activate per-residue no-fit RMSD calculation.
perresout <perresfile> Write per-residue RMSD to <perresfile>.
perresavg <avgfile> Write average per-residue RMSDs to <avgfile>.
range <res range> Calculate per-residue RMSDs for residues in <res range> (default all solute residues).
refrange <ref range> Calculate per-residue RMSDs to reference residues in <ref range> (use <res range> if not specified).
perresmask <additional mask> By default residues are selected using the mask ’:X’ where X is residue number; this appends <additional mask> to the mask expression.
perrescenter Translate residues to a common center of mass prior to calculating RMSD.
perresinvert Make X-axis residue number instead of frame number.

Data Sets Created:
<name> RMSD of atoms in mask to reference.
<name>[RM] (savematrices only) Rotation matrices of target to reference.
<name>[res] (perres only) Per-residue RMSDs; index is residue number.
<name>[Avg] (perres only) Average per-residue RMSD for each residue.
<name>[Stdev] (perres only) Standard deviation of RMSD for each residue.

Note that perres data sets are not generated until run is called.

Calculate the coordinate RMSD of input frames to a reference frame (or reference trajectory). Both <mask> and <refmask> must specify the same number of atoms, otherwise an error will occur.

For example, say you have a trajectory and you want to calculate RMSD to two separate reference structures. To calculate the best-fit RMSD of the C, CA, and N atoms of residues 1 to 20 in each frame to the C, CA, and N atoms of residues 3 to 23 in StructX.crd, and then calculate the no-fit RMSD of residue 7 to residue 7 in another structure named Struct-begin.rst7, writing both results to Grace-format file “rmsd1.agr”:

reference StructX.crd [structX]
reference md_begin.rst7 [struct0]
rmsd BB :1-20@C,CA,N ref [structX] :3-23@C,CA,N out rmsd1.agr
rmsd Res7 :7 ref [struct0] out rmsd1.agr nofit

Per-residue RMSD calculation
If the perres keyword is specified, after the initial RMSD calculation the no-fit RMSD of specified residues is also calculated. So for example:

rmsd :10-260 reference perres perresout PRMS.dat range 190-211 perresmask &!(@H=)

will first perform a best-fit RMSD calculation to the first specified reference structure using residues 10 to 260, then calculate the no-fit RMSD of residues 190 to 211 (excluding any hydrogen atoms), writing the results to PRMS.dat. Two additional recommendations for the ’perres’ option: 1) try not including backbone atoms by using the ’perresmask’ keyword, e.g. “perresmask &!@H,N,CA,HA,C,O”, and 2) try using the ’perrescenter’ keyword, which centers each residue prior to the ’nofit’ calculation; this is useful for isolating changes in residue conformation.