Provided by: gromacs-data_4.6.5-1build1_all bug

NAME
       genconf - multiplies a conformation in 'random' orientations

       VERSION 4.6.5


SYNOPSIS
       genconf  -f  conf.gro  -o  out.gro  -trj traj.xtc -[no]h -[no]version -nice int -nbox vector -dist vector
       -seed int -[no]rot -[no]shuffle -[no]sort -block int -nmolat int -maxrot vector -[no]renumber


DESCRIPTION
        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.


FILES
       -f conf.gro Input
        Structure file: gro g96 pdb tpr etc.

       -o out.gro Output
        Structure file: gro g96 pdb etc.

       -trj traj.xtc Input, Opt.
        Trajectory: xtc trr trj gro g96 pdb cpt


OTHER OPTIONS
       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version info and quit

       -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]rotno
        Randomly rotate conformations

       -[no]shuffleno
        Random shuffling of molecules

       -[no]sortno
        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]renumberyes
        Renumber residues


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


SEE ALSO
       gromacs(7)

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

                                                 Mon 2 Dec 2013                                       genconf(1)