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       g_sdf  -  calculates  the  spatial  distribution  function (faster than

       VERSION 4.0.1


       g_sdf  -f  traj.xtc  -n  index.ndx  -s  topol.tpr  -o  gom_plt.dat   -r
       refmol.gro  -[no]h  -nice  int  -b  time  -e  time  -dt  time -mode int
       -triangle vector -dtri vector -bin real -grid vector


       g_sdf calculates the spatial distribution function (SDF) of  a  set  of
       atoms  within  a  coordinate  system  defined  by three atoms. There is
       single body, two body and  three  body  SDF  implemented  (select  with
       option  -mode).  In the single body case the local coordinate system is
       defined by using a triple of atoms from one single  molecule,  for  the
       two  and  three  body  case the configurations are dynamically searched
       complexes of two or  three  molecules  (or  residues)  meeting  certain
       distance consitions (see below).

       The  program  needs a trajectory, a GROMACS run input file and an index
       file to work.  You have to setup 4 groups  in  the  index  file  before
       using g_sdf:

       The  first  three  groups are used to define the SDF coordinate system.
       The programm will dynamically generate the atom  tripels  according  to
       the  selected  -mode: In -mode 1 the triples will be just the 1st, 2nd,
       3rd, ... atoms from groups 1, 2 and 3. Hence the nth entries in  groups
       1,  2  and 3 must be from the same residue. In -mode 2 the triples will
       be 1st, 2nd, 3rd, ... atoms from groups 1 and 2 (with the  nth  entries
       in groups 1 and 2 having the same res-id).  For each pair from groups 1
       and 2  group 3 is searched for an atom meeting the distance  conditions
       set  with -triangle and -dtri relative to atoms 1 and 2. In -mode 3 for
       each atom in group 1 group 2  is  searched  for  an  atom  meeting  the
       distance  condition  and  if a pair is found group 3 is searched for an
       atom meeting the further conditions. The triple will only  be  used  if
       all three atoms have different res-id’s.

       The  local  coordinate  system  is  always  defined using the following
       scheme: Atom 1 will be used as the point of origin for the SDF. Atom  1
       and 2 will define the principle axis (Z) of the coordinate system.  The
       other two axis will be defined inplane (Y) and normal (X) to the  plane
       through Atoms 1, 2 and 3. The fourth group contains the atoms for which
       the SDF will be evaluated.

       For -mode 2 and 3 you have to define the distance conditions for the  2
       resp.  3  molecule  complexes  to  be  searched for using -triangle and

       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
       Volume of the SDF grid will be V=x*y*z  (nm3).  Use  -bin  to  set  the
       binwidth for grid.

       The  output  will  be  a  binary 3D-grid file (gom_plt.dat) in the .plt
       format that can be be read directly by gOpenMol.  The  option  -r  will
       generate  a  .gro file with the reference molecule(s) transfered to the
       SDF coordinate system. Load this file into gOpenMol and display the SDF
       as  a  contour  plot  (see  for
       further documentation).

       For further information about SDF’s have a look at: A. Vishnyakov,  JPC
       A, 105, 2001, 1702 and the references cited within.


       -f traj.xtc Input
        Trajectory: xtc trr trj gro g96 pdb cpt

       -n index.ndx Input
        Index file

       -s topol.tpr Input, Opt.
        Structure+mass(db): tpr tpb tpa gro g96 pdb

       -o gom_plt.dat Output
        Generic data file

       -r refmol.gro Output, Opt.
        Structure file: gro g96 pdb


        Print help info and quit

       -nice int 19
        Set the nicelevel

       -b time 0
        First frame (ps) to read from trajectory

       -e time 0
        Last frame (ps) to read from trajectory

       -dt time 0
        Only use frame when t MOD dt = first time (ps)

       -mode int 1
        SDF in [1,2,3] particle mode

       -triangle vector 0 0 0
        r(1,3), r(2,3), r(1,2)

       -dtri vector 0.03 0.03 0.03
        dr(1,3), dr(2,3), dr(1,2)

       -bin real 0.05
        Binwidth for the 3D-grid (nm)

       -grid vector 1 1 1
        Size of the 3D-grid (nm,nm,nm)



       More      information     about     GROMACS     is     available     at

                                Thu 16 Oct 2008                       g_sdf(1)