xenial (1) gmx-genconf.1.gz

Provided by: gromacs-data_5.1.2-1ubuntu1_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] [-[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/>.


       2015, GROMACS development team