NAME
g_sdf - calculates the spatial distribution function (faster than
g_spatial)
VERSION 4.0.1
SYNOPSIS
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
DESCRIPTION
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
-dtri.
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 http://www.csc.fi/gopenmol/index.phtml 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.
FILES
-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
OTHER OPTIONS
-[no]hno
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)
SEE ALSO
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 g_sdf(1)