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gmx-genconf(1)			GROMACS Manual			gmx-genconf(1)

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

SYNOPSIS
       gmx genconf [-f [<.gro/.g96/...>]] [-o [<.gro/.g96/...>]]
		   [-trj [<.xtc/.trr/...>]] [-nice <int>] [-nbox <vector>]
		   [-dist <vector>] [-seed <int>] [-[no]rot] [-[no]shuffle]
		   [-[no]sort] [-block <int>] [-nmolat <int>]
		   [-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
       interspaces 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
       input 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 and output files:

       -f [<.gro/.g96/...>] (conf.gro) (Input)
	   Structure file: gro g96 pdb brk ent esp tpr tpb tpa

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

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

       Other options:

       -nice <int> (0)
	   Set the nicelevel

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

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

       -seed <int> (0)
	   Random generator seed, if 0 generated from the time

       -[no]rot	 (no)
	   Randomly rotate conformations

       -[no]shuffle  (no)
	   Random shuffling of molecules

       -[no]sort  (no)
	   Sort molecules on X coord

       -block <int> (1)
	   Divide the box in blocks on this number of cpus

       -nmolat <int> (3)
	   Number of atoms per molecule, assumed to start from 0. If  you  set
       this wrong, it will screw up your system!

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

       -[no]renumber  (yes)
	   Renumber residues

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

SEE ALSO
       gromacs(7)

       More   information  about  GROMACS  is  available  at  <http://www.gro‐
       macs.org/>.

VERSION 5.0.6							gmx-genconf(1)

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