atomicfluct | rmsf

Compute the atomic positional fluctuations.

atomicfluct [out <filename>] [<mask>] [byres | byatom | bymask] [bfactor] [calcadp [adpout <file>]] [start <start>] [stop <stop>] [offset <offset>]

out <filename> Write data to file named <filename>
[<mask>] Calculate fluctuations for atoms in <mask> (all if not specified).
byres Output the average (mass-weighted) fluctuation by residue.
bymask Output the average (mass-weighted) fluctuation for all atoms in <mask>.
byatom (default) Output the fluctuation by atom.
[bfactor] Calculate atomic positional fluctuations squared and weight by  \frac{8}{3} \pi ^2 ;this is similar but not necessarily equivalent to the calculation of crystallographic B-factors.
[calcadp [adpout <file>]] Calculate anisotropic displacement parameters and optionally output them to <file>. [<start>] Frame to begin calculation at (default 1).
[<stop>] Frame to end calculation at (default last).
[<offset>] Frames to skip between calculations (default 1).

Compute the atomic positional fluctuations (also referred to as root-mean-square fluctuations, RMSF) for atoms specified in the <mask>. Note that RMS fitting is not done implicitly. If you want fluctuations without rotations or translations (for example to the average structure), perform an RMS fit to the average structure (best) or the first structure (see rmsd) prior to this calculation. The units are (Å) for RMSF or \AA ^2 \times \frac{8}{3} \pi ^2 if bfactor is specified.

If byres or bymask are specified, the mass-weighted average of atomic fluctuations of each atom for either each residue or the entire mask will be calculated respectively:

\text{Fluct}=\frac{\sum \text{AtomFluct}_i \times \text{Mass}_i}{\sum \text{Mass}_i}

If calcadp is specified, anisotropic displacement factors for atoms will be calculated and written to the file specified by adpout (or STDOUT if not specified) using PDB ANISOU record format. Note that calcadp automatically implies bfactor.

With cpptraj it is possible to perform coordinate averaging, the fit to average coordinates, and the atomic fluctuation calculation in a single execution like so:

parm myparm.parm7
 trajin mytrajectory.crd
 rms first
 average crdset MyAvg
 rms ref MyAvg
 atomicfluct out fluct.agr

To write the mass-weighted B-factors for the protein backbone atoms C, CA, and N, averaged by residue use the command:
atomicfluct out back.agr @C,CA,N byres bfactor

To write the RMSF or atomic positional fluctuations of the same atoms, use the command:
atomicfluct out backbone-atoms.agr @C,CA,N