Last update: 12.09.2007 (added eef, fixed amber6 parm detection bug in epl)

This is set of scripts/programs for processing and analysis of MD trajectories.
There may be errors and bugs in the code - use at your own risk.

I'm trying to rewrite these to python (dl_epl.py is the first one) - after it will
be done (probably never) i'll provide better documentation.

The code is in C, heavily commented. Also, please consult the respective README file
for each program for more detailed information.

The source can be downloaded from
http://lubos.vrbka.net/miscellaneous
feel free to spread it if you wish. You can contact me via e-mail at
lubos (_at_) vrbka (_dot_) net

Install by issuing
    make
The resulting binaries will be placed to exe/ subdirectory
The programs require -lz (zlib) and -lm (math libraries) to be available.

eef
    calculates electric field along a given vector from MD data
    
epl
    extracts coordinates from amber trajectories
dl_epl.py
    extracts coordinates from DLPOLY trajectories
epl_b2t
    converts extracted coords in binary format to text

edipl
    extracts induced dipoles from amber trajectories (our local version only)
edipl_b2t
    converts extracted induced dipoles from binary to text

difc
    provides estimate of a diffusion constant for a particle
dipp
    calculates induced dipole profile
dp
    calculates density profile
gr
    calculates radial distribution function
gr2
    calculates pair radial distribution function
gr2_surf, gr2_bulk
    the same analysis restricted in space - useful for analysis of bulk and surface
    g(r)'s in slab simulations
chgp
    calculates charge profiles
orient
    calculates orientation with respect to some axis
orient_surf, orient_bulk
    the same analysis restricted in space - useful for analysis of bulk and surface
    in slab simulations
orient3
    calculates orientation for (rigid) water molecules