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GMX-GENCONF(1)			    GROMACS			GMX-GENCONF(1)

NAME
       gmx-genconf - Multiply a	conformation in	'random' orientations

SYNOPSIS
	  gmx genconf [-f [_.gro/.g96/..._]] [-trj [_.xtc/.trr/..._]]
		      [-o [_.gro/.g96/..._]] [-nbox _vector_] [-dist _vector_]
		      [-seed _int_] [-[no]rot] [-maxrot	_vector_]
		      [-[no]renumber]

DESCRIPTION
       gmx  genconf multiplies a given coordinate file by simply stacking them
       on top of each other, like a small child	playing	 with  wooden  blocks.
       The  program  makes a grid of user-defined proportions (-nbox), and in-
       terspaces the grid point	with an	extra space -dist.

       When option -rot	is used	the program does not check for overlap between
       molecules  on grid points. It is	recommended to make the	box in the in-
       put file	at least as big	as the coordinates + van der Waals radius.

       If the optional trajectory file is given, conformations are not	gener-
       ated, but read from this	file and translated appropriately to build the
       grid.

OPTIONS
       Options to specify input	files:

       -f [<.gro/.g96/^a|>] (conf.gro)
	      Structure	file: gro g96 pdb brk ent esp tpr

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

       Options to specify output files:

       -o [<.gro/.g96/^a|>] (out.gro)
	      Structure	file: gro g96 pdb brk ent esp

       Other options:

       -nbox <vector> (1 1 1)
	      Number of	boxes

       -dist <vector> (0 0 0)
	      Distance between boxes

       -seed <int> (0)
	      Random generator seed (0 means generate)

       -[no]rot	(no)
	      Randomly rotate conformations

       -maxrot <vector>	(180 180 180)
	      Maximum random rotation

       -[no]renumber (yes)
	      Renumber residues

KNOWN ISSUES
       o The program should allow for random displacement of lattice points.

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-GENCONF(1)

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

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