Dihedral principal component analysis

gmx angle, gmx covar, gmx anaeig

Principal component analysis can be performed in dihedral space 172 using GROMACS. You start by defining the dihedral angles of interest in an index file, either using gmx mk_angndx or otherwise. Then you use the gmx angle program with the -or flag to produce a new trr file containing the cosine and sine of each dihedral angle in two coordinates, respectively. That is, in the trr file you will have a series of numbers corresponding to: cos(\(\phi_1\)), sin(\(\phi_1\)), cos(\(\phi_2\)), sin(\(\phi_2\)), …, cos(\(\phi_n\)), sin(\(\phi_n\)), and the array is padded with zeros, if necessary. Then you can use this trr file as input for the gmx covar program and perform principal component analysis as usual. For this to work you will need to generate a reference file (tpr, gro, pdb etc.) containing the same number of “atoms” as the new trr file, that is for \(n\) dihedrals you need 2\(n\)/3 atoms (rounded up if not an integer number). You should use the -nofit option for gmx covar since the coordinates in the dummy reference file do not correspond in any way to the information in the trr file. Analysis of the results is done using gmx anaeig.