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

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                    GMX-GENCONF(1)

gmxgenconf 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.

       • The program should allow for random displacement of lattice points.

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

       Options to specify input files:

       -f[<.gro/.g96/...>](conf.gro)
              Structure file: grog96pdb brk ent esp tpr-trj[<.xtc/.trr/...>](traj.xtc)(Optional)
              Trajectory: xtctrrcptgrog96pdbtng

       Options to specify output files:

       -o[<.gro/.g96/...>](out.gro)
              Structure file: grog96pdb brk ent esp

       Other options:

       -nbox<vector>(111)
              Number of boxes

       -dist<vector>(000)
              Distance between boxes

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

       -[no]rot(no)
              Randomly rotate conformations

       -maxrot<vector>(180180180)
              Maximum random rotation

       -[no]renumber(yes)
              Renumber residues

gmx(1)

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

          gmx genconf [-f[<.gro/.g96/...>]] [-trj[<.xtc/.trr/...>]]
                      [-o[<.gro/.g96/...>]] [-nbox<vector>] [-dist<vector>]
                      [-seed<int>] [-[no]rot] [-maxrot<vector>]
                      [-[no]renumber]