Dihedral PCA

Stepwise instructions

1. Use mk_angndx or text editor to generate an index file for the atoms involved in the chosen dihedral angles.

2. Extract the angles from trajectory using the index file from step 1., e.g., dangle.ndx, in a command like:

g_angle -f foo.xtc -s foo.tpr -n dangle.ndx -or dangle.trr -type dihedral

where the output is dangle.trr.

3. Make an index file, named as covar.ndx, which necessarily contains one group of atom 1 to integer(2*N/3), where N is the number of dihedral angles. For example, for a peptide of 5 dihedral angles, the contents of covar.ndx should be

   [ foo ]
   1   2   3   4

4. Get one of the .gro files that contains integer(2*N/3) atoms. Box size and atom coordinates don't matter. For example,

trjconv -s foo.tpr -f dangle.trr -o resized.gro -n covar.ndx -e 0

5. Perform the diagonalization with a command like

g_covar -f dangle.trr -n covar.ndx -ascii -xpm -nofit -nomwa -noref -nopbc -s resized.gro

where the outputs are eigenval.xvg, eigenvec.trr, covar.log, covar.dat, and covar.xpm.

6. To get a PMF along one eigenvector use a command like

g_anaeig -v eigenvec.trr -f dangle.trr -s resized.gro -first X -last X -proj proj-1

where X is the serial number of the eigenvector. To visualize the result, use

xmgrace proj-X.xvg

7. To get a free energy landscape for projections along two eigenvectors, use a command like

g_anaeig -v eigenvec.trr -f dangle.trr -noxvgr -s resized.gro -first X -last Y -2d 2dproj_X_Y.xvg

where X and Y are the serial numbers of the eigenvectors.

8. To transform such data into free energy landscape terms, we divide the 2D landscape with grid and count the number of conformations inside each grid. An awk script for such purpose has been posted here.  The g_sham program (specifying the -notime option) can also be used to generate a 2-D plot of a free energy surface.