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] [-[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 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, 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

       gmx(1)

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

COPYRIGHT

       2015, GROMACS development team