This is part of the colvar module

Calculate the PCA components ( see [100] and [98] ) for a number of provided eigenvectors and an average structure. Performs optimal alignment at every step and reports the rmsd so you know if you are far or close from the average structure. It takes the average structure and eigenvectors in form of a pdb. Note that beta and occupancy values in the pdb are neglected and all the weights are placed to 1 (differently from the RMSD colvar for example)

Description of components

By default the value of the calculated quantity can be referenced elsewhere in the input file by using the label of the action. Alternatively this Action can be used to calculate the following quantities by employing the keywords listed below. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.

Quantity	Description
eig	the projections on each eigenvalue are stored on values labeled eig-1, eig-2, ...
residual	the distance of the present configuration from the configuration supplied as AVERAGE in terms of mean squared displacement after optimal alignment

Compulsory keywords

AVERAGE	a file in pdb format containing the reference structure and the atoms involved in the CV.
EIGENVECTORS	a file in pdb format containing the reference structure and the atoms involved in the CV.

Options

NUMERICAL_DERIVATIVES

( default=off ) calculate the derivatives for these quantities numerically

NOPBC

( default=off ) ignore the periodic boundary conditions when calculating distances

SQUARED_ROOT

( default=off ) This should be set if you want RMSD instead of mean squared displacement

Examples

PCARMSD AVERAGE=file.pdb EIGENVECTORS=eigenvectors.pdb

The input is taken so to be compatible with the output you get from g_covar utility of gromacs (suitably adapted to have a pdb input format). The reference configuration (file.pdb) will thus be in a file that looks something like this:

TITLE     Average structure
MODEL        1
ATOM      1  CL  ALA     1       1.042  -3.070   0.946  1.00  0.00
ATOM      5  CLP ALA     1       0.416  -2.033   0.132  1.00  0.00
ATOM      6  OL  ALA     1       0.415  -2.082  -0.976  1.00  0.00
ATOM      7  NL  ALA     1      -0.134  -1.045   0.677  1.00  0.00
ATOM      9  CA  ALA     1      -0.774   0.053   0.003  1.00  0.00
TER
ENDMDL

while the eigenvectors will be in a pdb file (eigenvectors.pdb) that looks something like this:

TITLE     frame t= -1.000
MODEL        1
ATOM      1  CL  ALA     1       1.194  -2.988   0.724  1.00  0.00
ATOM      5  CLP ALA     1      -0.996   0.042   0.144  1.00  0.00
ATOM      6  OL  ALA     1      -1.246  -0.178  -0.886  1.00  0.00
ATOM      7  NL  ALA     1      -2.296   0.272   0.934  1.00  0.00
ATOM      9  CA  ALA     1      -0.436   2.292   0.814  1.00  0.00
TER
ENDMDL
TITLE     frame t= 0.000
MODEL        1
ATOM      1  CL  ALA     1       1.042  -3.070   0.946  1.00  0.00
ATOM      5  CLP ALA     1      -0.774   0.053   0.003  1.00  0.00
ATOM      6  OL  ALA     1      -0.849  -0.166  -1.034  1.00  0.00
ATOM      7  NL  ALA     1      -2.176   0.260   0.563  1.00  0.00
ATOM      9  CA  ALA     1       0.314   1.825   0.962  1.00  0.00
TER
ENDMDL