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GMX-SPATIAL(1)			    GROMACS			GMX-SPATIAL(1)

NAME
       gmx-spatial - Calculate the spatial distribution	function

SYNOPSIS
	  gmx spatial [-s [_.tpr/.gro/..._]] [-f [_.xtc/.trr/..._]] [-n	[_.ndx_]]
		      [-b _time_] [-e _time_] [-dt _time_] [-[no]w] [-[no]pbc]
		      [-[no]div] [-ign _int_] [-bin _real_] [-nab _int_]

DESCRIPTION
       gmx spatial calculates the spatial distribution function	and outputs it
       in a form that can be read by VMD as Gaussian98	cube  format.	For  a
       system of 32,000	atoms and a 50 ns trajectory, the SDF can be generated
       in about	30 minutes, with most of the time dedicated to	the  two  runs
       through	trjconv	that are required to center everything properly.  This
       also takes a whole bunch	of space (3 copies of  the  trajectory	file).
       Still, the pictures are pretty and very informative when	the fitted se-
       lection is properly made.  3-4 atoms in a widely	mobile group  (like  a
       free amino acid in solution) works well,	or select the protein backbone
       in a stable folded structure to get the SDF of solvent and look at  the
       time-averaged  solvation	shell.	It is also possible using this program
       to generate the SDF based on some arbitrary Cartesian coordinate. To do
       that, simply omit the preliminary gmx trjconv steps.

       Usage:

       1. Use gmx make_ndx to create a group containing	the atoms around which
       you want	the SDF	2. gmx trjconv -s a.tpr	-f a.tng -o  b.tng  -boxcenter
       tric  -ur  compact  -pbc	none 3.	gmx trjconv -s a.tpr -f	b.tng -o c.tng
       -fit rot+trans 4. run gmx spatial on the	c.tng output of	step  #3.   5.
       Load grid.cube into VMD and view	as an isosurface.

       Note  that systems such as micelles will	require	gmx trjconv -pbc clus-
       ter between steps 1 and 2.

   Warnings
       The SDF will be generated for a cube that contains all bins  that  have
       some  non-zero  occupancy.  However, the	preparatory -fit rot+trans op-
       tion to gmx trjconv implies that	 your  system  will  be	 rotating  and
       translating  in	space  (in  order  that	 the selected group does not).
       Therefore the values that are returned will only	be valid for some  re-
       gion  around  your  central group/coordinate that has full overlap with
       system volume throughout	the entire translated/rotated system over  the
       course  of the trajectory.  It is up to the user	to ensure that this is
       the case.

   Risky options
       To reduce the amount of space and time required,	you  can  output  only
       the  coords  that  are going to be used in the first and	subsequent run
       through gmx trjconv.  However, be sure to set the -nab option to	a suf-
       ficiently  high	value since memory is allocated	for cube bins based on
       the initial coordinates and the -nab option value.

OPTIONS
       Options to specify input	files:

       -s [<.tpr/.gro/^a|>] (topol.tpr)
	      Structure+mass(db): tpr gro g96 pdb brk ent

       -f [<.xtc/.trr/^a|>] (traj.xtc)
	      Trajectory: xtc trr cpt gro g96 pdb tng

       -n [<.ndx>] (index.ndx) (Optional)
	      Index file

       Other options:

       -b <time> (0)
	      Time of first frame to read from trajectory (default unit	ps)

       -e <time> (0)
	      Time of last frame to read from trajectory (default unit ps)

       -dt <time> (0)
	      Only use frame when t MOD	dt = first time	(default unit ps)

       -[no]w (no)
	      View output .xvg,	.xpm, .eps and .pdb files

       -[no]pbc	(no)
	      Use periodic boundary conditions for computing distances

       -[no]div	(yes)
	      Calculate	and apply the divisor for  bin	occupancies  based  on
	      atoms/minimal  cube  size.  Set as TRUE for visualization	and as
	      FALSE (-nodiv) to	get accurate counts per	frame

       -ign <int> (-1)
	      Do not display this number of outer cubes	(positive  values  may
	      reduce boundary speckles;	-1 ensures outer surface is visible)

       -bin <real> (0.05)
	      Width of the bins	(nm)

       -nab <int> (4)
	      Number of	additional bins	to ensure proper memory	allocation

KNOWN ISSUES
       o When  the  allocated memory is	not large enough, a segmentation fault
	 may occur.

       o This is usually detected

       o and the program is halted prior to the	fault while displaying a warn-
	 ing message

       o suggesting the	use of the -nab	(Number	of Additional Bins)

       o option.  However, the program does not	detect all such	events.	If you
	 encounter a

       o segmentation fault, run it again

       o with an increased -nab	value.

SEE ALSO
       gmx(1)

       More    information    about    GROMACS	  is	available    at	    <-
       http://www.gromacs.org/>.

COPYRIGHT
       2021, GROMACS development team

2021.2				 May 05, 2021			GMX-SPATIAL(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | KNOWN ISSUES | SEE ALSO | COPYRIGHT

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