Synopsis

This analyzer calculates the mean-squared-displacement vs. time for the center of mass of a specific molecular species. It properly takes into account the effects of periodic boundary conditions by reconstructing continuous trajectories for the molecular center of mass. "Center of mass" is calculated by weighting each atom in the molecule equally, without using any actual atomic masses, and thus might more properly called the geometric center.

Parameters

The parameter file format is:

ComMSD{
  interval           int
  outputFileName     string
  speciesId          int
  capacity           int
}

with parameters

interval	number of steps between data samples
outputFileName	name of output file
speciesId	integer index of molecule species
capacity	number of time separations in output, and number of positions stored in history

Output

At the end of the simulation:

Parameters are echoed to file {outputFileName}.prm.

Final results for MSD vs. number of samples are output to the file {outputFileName}.dat.