[gmx-users] g_sdf v0.6

[Christoph Freudenberger]

Hi there,

I am happy to announce the first version of g_sdf. I don't want to upload
the program to the contribution site yet, because I expect that a
few thing have to be considered first.
I'd like to invite anybody to have a look at the code and try the program.
Especially I'd ask the gmx-team to check the code for consistency with
the rest of gmx.

OK, let me give you the description of the program:

                                 :-)  g_sdf  (-:

DESCRIPTION:

g_sdf calculates the spatial distribution function (SDF) of a set of atoms
relative to a molecule of reference.

WARNING: This version of g_sdf is developed to study a system that contains one
molecule of reference only, but it should be extendable to work with multiple
reference molecules.

You have to provide two groups from an index file:

The first group defines the reference molecule. It can contain any number of
atoms but only the first three atoms will be used to define the molecular
coordinate system. Selection of these atoms is in principle arbitrary. Atom 1
will be used as the default point of origin for the SDF. Atom 1 and 2 will
define the principle axis of the coordinate system. The other axis will be
defined inplane and normal to the plane through Atoms 1, 2 and 3. With option
-cog the SDF will be computed with respect to the geometric center of the
reference group. This is useful for analysis of larger molecules. More than
three atoms should be given in the group then.

The second group contains the atoms for which the SDF will be evaluated.

The SDF will be sampled in cartesian coordinates. Use '-grid x y z' to define
the size of the SDF grid around the reference molecule. The SDF is evaluated
within (-x < dx < x) from the point of origin (and for y and z respectivly).
Hence the default values will result in grid of 1 nm^3. Use -bin to set the
binwidth for each coordinate.

The output will be a binary 3D-grid file (grid.dat) that can be be read
directly by gOpenMol. The option -r will generate a .gro file with the
reference group transfered to the molecular coordinate system. Load this file
into gOpenMol and display the SDF as a contour plot (see
http://www.csc.fi/gopenmol/index.phtml for futher documentation).

Option     Filename  Type          Description
------------------------------------------------------------
   -f       traj.xtc  Input         Generic trajectory: xtc trr trj gro g96 pdb
   -n      index.ndx  Input         Index file
   -s      topol.tpr  Input, Opt.   Structure+mass(db): tpr tpb tpa gro g96 pdb
   -o       grid.dat  Output        Generic data file
   -r     refmol.gro  Output, Opt.  Generic structure: gro g96 pdb

       Option   Type  Value  Description
------------------------------------------------------
       -[no]h   bool    yes  Print help info and quit
       -[no]X   bool     no  Use dialog box GUI to edit command line options
        -nice    int     19  Set the nicelevel
           -b   time     -1  First frame (ps) to read from trajectory
           -e   time     -1  Last frame (ps) to read from trajectory
          -dt   time     -1  Only use frame when t MOD dt = first time (ps)
     -[no]cog   bool     no  SDF with respect to the center of mass of ref group
         -bin vector 0.05 0.05 0.05  Binwidth for cathesian coordinates x,y,z
                             (nm,nm,nm)
        -grid vector 0.5 0.5 0.5  Maximum distance in x,y,z (nm,nm,nm) to be
                             considered
-------------------------------------------------------

Right now I see two major problems with the program:
1. I cannot provide a bullet proof Makefile because I don't know much about make.
    Actually I just added a few lines to the Makefile in $GMXDATA/template and
    compiled it this way.
    Any help to provide a general installation procedure is appreciated.
2. The actual version can only handle one single reference molecule.
    Any sugestions on how this could be extended are also appreciated.

If you want to try the program, just drop me a line and I'll send you the code.
If you're just curious how the graphics look like, feel free to request some
jpg's.

best regards
-- 
Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785