This directory contains the files to compute and visualize the all-atom
vibrational modes of phosphoglycolate phosphatase (2hi0). To do the
computation simply run the Run_lmod-vib script in the lmod subdirectory.
The only parameter that you might want to change is the number of CPUs,
it is set to 16. If you want to vary other parameters, consult the 
detailed documentation in the Amber User Manual.

Notes:
(1) Running LMOD calculations requires that the parameter file is 
    processed by the 'lmod' command in parmed.
(2) The primary output is in the file lmod-vib_trajectory, it can be 
    converted to dcd via 'cpptraj -p 2hi0.parm7 -y lmod-vib_trajectory
    -x 2hi0-lmod-vibmodes.dcd'
(3) The last mode is always a pseudo mode, which is a random mixture of
    all the calculated modes.

Animation: Unlike CA-based network models, LMOD generates all-atom 
normal modes of vibration. The animation subdirectory has two Pymol
examples to animate the modes.

(1) pymol 2hi0.pdb
Pymol> load_traj 2hi0-lmod-vibmodes.dcd
Pymol> run color.py

Running the color command takes a while, but it'll color the frames such
that the animation changes color with every vibrational mode. The end
result is saved in the 2hi0-vibmodes-anim.pse Pymol session.

(2) pymol run-modevectors.pml -- 2hi0.pdb 2hi0-lmod-vibmodes.dcd 21 10

will produce a static representation of the normal modes represented by 
colored arrows placed on CA atoms. The length of the arrows is 
proportional to the magnitude of atomic movement. No arrow means less
atomic movement than a cutoff. This representation is saved in the
2hi0-vibmodes-arrows.pse Pymol session. On the command line 21 is 20 
modes plus one pseudo mode, and 10 means that there are 10 frames in
one half vibration. These are the conflib_size=total_low_modes=
explored_low_modes=20 and number_lmod_moves=10 parameters in the
Run_lmod-vib script.

In the run-modevectors.pml script the 'cutoff' parameter (set to 0.7) 
determines if an arrow will be drawn at a CA atom depending on whether
that atom moves more than cutoff Angstroms in that particular mode. The 
other important parameter is 'factor' (set to 5.0), which is a scaling
factor applied to the length of the arrows and can be used to adjust the
graphics.

