# Covariance analysis¶

Covariance analysis, also called principal component analysis or essential dynamics 169, can find correlated motions. It uses the covariance matrix \(C\) of the atomic coordinates:

where \(M\) is a diagonal matrix containing the masses of the atoms (mass-weighted analysis) or the unit matrix (non-mass weighted analysis). \(C\) is a symmetric \(3N \times 3N\) matrix, which can be diagonalized with an orthonormal transformation matrix \(R\):

The columns of \(R\) are the eigenvectors, also called principal or essential modes. \(R\) defines a transformation to a new coordinate system. The trajectory can be projected on the principal modes to give the principal components \(p_i(t)\):

The eigenvalue \(\lambda_i\) is the mean square fluctuation of principal component \(i\). The first few principal modes often describe collective, global motions in the system. The trajectory can be filtered along one (or more) principal modes. For one principal mode \(i\) this goes as follows:

When the analysis is performed on a macromolecule, one often wants to remove the overall rotation and translation to look at the internal motion only. This can be achieved by least square fitting to a reference structure. Care has to be taken that the reference structure is representative for the ensemble, since the choice of reference structure influences the covariance matrix.

One should always check if the principal modes are well defined. If the
first principal component resembles a half cosine and the second
resembles a full cosine, you might be filtering noise (see below). A
good way to check the relevance of the first few principal modes is to
calculate the overlap of the sampling between the first and second half
of the simulation. **Note** that this can only be done when the same
reference structure is used for the two halves.

A good measure for the overlap has been defined in 170. The elements of the covariance matrix are proportional to the square of the displacement, so we need to take the square root of the matrix to examine the extent of sampling. The square root can be calculated from the eigenvalues \(\lambda_i\) and the eigenvectors, which are the columns of the rotation matrix \(R\). For a symmetric and diagonally-dominant matrix \(A\) of size \(3N \times 3N\) the square root can be calculated as:

It can be verified easily that the product of this matrix with itself gives \(A\). Now we can define a difference \(d\) between covariance matrices \(A\) and \(B\) as follows:

where tr is the trace of a matrix. We can now define the overlap \(s\) as:

The overlap is 1 if and only if matrices \(A\) and \(B\) are identical. It is 0 when the sampled subspaces are completely orthogonal.

A commonly-used measure is the subspace overlap of the first few eigenvectors of covariance matrices. The overlap of the subspace spanned by \(m\) orthonormal vectors \({\bf w}_1,\ldots,{\bf w}_m\) with a reference subspace spanned by \(n\) orthonormal vectors \({\bf v}_1,\ldots,{\bf v}_n\) can be quantified as follows:

The overlap will increase with increasing \(m\) and will be 1 when set \({\bf v}\) is a subspace of set \({\bf w}\). The disadvantage of this method is that it does not take the eigenvalues into account. All eigenvectors are weighted equally, and when degenerate subspaces are present (equal eigenvalues), the calculated overlap will be too low.

Another useful check is the cosine content. It has been proven that the the principal components of random diffusion are cosines with the number of periods equal to half the principal component index 170, 171. The eigenvalues are proportional to the index to the power \(-2\). The cosine content is defined as:

When the cosine content of the first few principal components is close to 1, the largest fluctuations are not connected with the potential, but with random diffusion.

The covariance matrix is built and diagonalized by gmx covar. The principal components and overlap (and many more things) can be plotted and analyzed with gmx anaeig. The cosine content can be calculated with gmx analyze.