Provided by: gromacs-data_2025.2-1_all bug

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
       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 generated, but read from this file and
       translated appropriately to build the grid.


OPTIONS
       Options to specify input files:

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

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

       Options to specify output files:

       -o [<.gro/.g96/...>] (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
       • 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
       2025, GROMACS development team

2025.2                                            May 12, 2025                                    GMX-GENCONF(1)