MSD (Mean Squared Displacement) Program

msd (source code available here) calculates the Mean Squared Displacement of a set of atoms as determined by their starting and instantaneous positions read from a COR or RCV file.

Here is the help info printed by the MSD program.

   msd [..options..] FREF [ {FMSD | *} [STEP] ]
       FREF  is input RCV or COR file with reference step
       FMSD  is input RCV or COR file with steps to calculate
                Mean Squared Displacement
          *  instructs program to use same file as FREF
       If FMSD not specified, program uses same name as FREF
       step  is step number to use as reference step
       -3          Output xx,yy,zz components of MSD
       -6          Output xx,yy,zz,yz,zx,xy components of MSD
       -r          Calculate MSD relative to previous step
       -i filist   Use ILIST file (first line:   ILIST n    - followed by
                   indices) to select atoms for MSD calculation.
       -b x0 y0 z0 x1 y1 z1
                   Only use atoms within box
       -d          Displace selected atoms to minimize MSD
       -h          Print output column headers
       -m          Switch atom order to minimize MSD.
       -p          Print out displacment obtained with previous option
       -w          Do not print warnings
    Calculates Mean Square Displacement for each step in file FMSD relative
    to step STEP in file FREF (default step is first in file).