Distances from reference configurations

One colvar that has been shown to be very successful in studying protein folding is the distance between the instantaneous configuration and a reference configuration - often the structure of the folded state. When the free energy of a protein is shown as a function of this collective variable there is a minima for low values of the CV, which is due to the folded state of the protein. There is then a second minima at higher values of the CV, which is the minima corresponding to the unfolded state.

A slight problem with this sort of collective variable is that there are many different ways of calculating the distance from a particular reference structure. The simplest - adding together the distances by which each of the atoms has been translated in going from the reference configuration to the instantaneous configuration - is not particularly sensible. A distance calculated in this way does not neglect translation of the center of mass of the molecule and rotation of the frame of reference. A common practice is thus to remove these components by calculating the RMSD distance between the reference and instantaneous configurations. This is not the only way to calculate the distance, however. One could also calculate the total amount by which a large number of collective variables change in moving from the reference to the instantaneous configurations. One could even combine RMSD distances with the amount the collective variables change. A full list of the ways distances can be measured in PLUMED is given below:

DRMSD	Calculate the distance RMSD with respect to a reference structure.
MULTI_RMSD	Calculate the RMSD distance moved by a number of separated domains from their positions in a reference structure.
PCARMSD	Calculate the PCA components for a number of provided eigenvectors and an average structure.
RMSD	Calculate the RMSD with respect to a reference structure.
TARGET	This function measures the Pythagorean distance from a particular structure measured in the space defined by some set of collective variables.

These options for calculating distances are re-used in a number of places in the code. For instance they are used in some of the analysis algorithms that are implemented in PLUMED and in PATH collective variables. Notice that most of these actions read the reference configuration from a PDB file. Be sure you understand how to format properly a PDB file to use used in PLUMED (see pdbreader).