convert trajectory files in many ways

do_dssp reads a trajectory file and computes the secondary structure for each time frame calling the dssp program.

Generalized Correlation for Biomolecular Dynamics (g_correlation) allows to compute both, linear or non-linear genearlized correlation coefficients. The accurate characterization of correlated motions would also improve the interpretation of NMR experiments and X-ray diffusive scattering data.

g_rms compares two structures by computing the root mean square deviation (RMSD)

g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions after (optionally) fitting to a reference frame.

g_sas computes hydrophobic, hydrophilic and total solvent accessible surface area.

g_gyrate computes the radius of gyration of a group of atoms and the radii of gyration about the x, y and z axes, as a function of time.

g_hbond computes and analyzes hydrogen bonds.

g_dist can calculate the distance between the centers of mass of two groups of atoms as a function of time.

g_energy extracts energy components or distance restraint data from an energy file.

g_rama selects the Phi/Psi dihedral combinations from your topology file and computes these as a function of time.

g_covar calculates and diagonalizes the (mass-weighted) covariance matrix.

g_cluster can cluster structures with several different methods.