g_spatial(1)

1g_spatial(1)              GROMACS suite, VERSION 4.5              g_spatial(1)
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NAME

6       g_spatial  - calculates the spatial distribution function (more control
7       than g_sdf)
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9       VERSION 4.5
10

SYNOPSIS

12       g_spatial -s topol.tpr -f traj.xtc  -n  index.ndx  -[no]h  -[no]version
13       -nice  int  -b  time -e time -dt time -[no]w -[no]pbc -[no]div -ign int
14       -bin real -nab int
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DESCRIPTION

17       g_spatial calculates the spatial distribution function and  outputs  it
18       in  a form that can be read by VMD as Gaussian98 cube format.  This was
19       developed from template.c (gromacs-3.3).  For a system of 32K atoms and
20       a  50ns  trajectory, the SDF can be generated in about 30 minutes, with
21       most of the time dedicated to the two runs  through  trjconv  that  are
22       required  to center everything properly.  This also takes a whole bunch
23       of space (3 copies of the xtc file).  Still, the  pictures  are  pretty
24       and  very  informative when the fitted selection is properly made.  3-4
25       atoms in a widely mobile group like a free amino acid in solution works
26       well,  or  select  the protein backbone in a stable folded structure to
27       get the SDF of solvent and look at the time-averaged  solvation  shell.
28       It  is  also  possible  using this program to generate the SDF based on
29       some arbitrarty Cartesian coordinate. To do that, simply omit the  pre‐
30       liminary trjconv steps.
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32       USAGE:
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34       1. Use make_ndx to create a group containing the atoms around which you
35       want the SDF
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37       2. trjconv -s a.tpr -f a.xtc -o b.xtc -center  tric  -ur  compact  -pbc
38       none
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40       3. trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans
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42       4. run g_spatial on the xtc output of step 3.
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44       5. Load grid.cube into VMD and view as an isosurface.
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46       ***  Systems such as micelles will require trjconv -pbc cluster between
47       steps 1 and 2
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49       WARNINGS:
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51       The SDF will be generated for a cube that contains all bins  that  have
52       some  non-zero  occupancy.   However,  the  preparatory  -fit rot+trans
53       option to trjconv implies that your system will be rotating and  trans‐
54       lating  in space (in order that the selected group does not). Therefore
55       the values that are returned will only be valid for some region  around
56       your  central group/coordinate that has full overlap with system volume
57       throughout the entire translated/rotated system over the course of  the
58       trajectory.  It is up to the user to ensure that this is the case.
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60       BUGS:
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62       When the allocated memory is not large enough, a segmentation fault may
63       occur. This is usually detected and the program is halted prior to  the
64       fault while displaying a warning message suggesting the use of the -nab
65       option. However, the program does not detect all such  events.  If  you
66       encounter  a  segmentation  fault,  run it again with an increased -nab
67       value.
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69       RISKY OPTIONS:
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71       To reduce the amount of space and time required, you  can  output  only
72       the  coords  that  are going to be used in the first and subsequent run
73       through trjconv.  However, be sure to set the -nab option to  a  suffi‐
74       ciently high value since memory is allocated for cube bins based on the
75       initial coords and the -nab (Number of Additional Bins) option value.
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FILES

79       -s topol.tpr Input
80        Structure+mass(db): tpr tpb tpa gro g96 pdb
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82       -f traj.xtc Input
83        Trajectory: xtc trr trj gro g96 pdb cpt
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85       -n index.ndx Input, Opt.
86        Index file
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OTHER OPTIONS

90       -[no]hno
91        Print help info and quit
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93       -[no]versionno
94        Print version info and quit
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96       -nice int 0
97        Set the nicelevel
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99       -b time 0
100        First frame (ps) to read from trajectory
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102       -e time 0
103        Last frame (ps) to read from trajectory
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105       -dt time 0
106        Only use frame when t MOD dt = first time (ps)
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108       -[no]wno
109        View output xvg, xpm, eps and pdb files
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111       -[no]pbcno
112        Use periodic boundary conditions for computing distances
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114       -[no]divyes
115        Calculate  and  apply  the  divisor  for  bin  occupancies  based   on
116       atoms/minimal  cube  size.  Set  as TRUE for visualization and as FALSE
117       (-nodiv) to get accurate counts per frame
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119       -ign int -1
120        Do not display this number of outer cubes (positive values may  reduce
121       boundary speckles; -1 ensures outer surface is visible)
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123       -bin real 0.05
124        Width of the bins in nm
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126       -nab int 4
127        Number of additional bins to ensure proper memory allocation
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NAME

SYNOPSIS

DESCRIPTION

FILES

OTHER OPTIONS

SEE ALSO