gmx genconf [-f [<.gro/.g96/...>]] [-trj [<.xtc/.trr/...>]] [-o [<.gro/.g96/...>]] [-nbox <vector>] [-dist <vector>] [-seed <int>] [-[no]rot] [-maxrot <vector>] [-[no]renumber]
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
and interspaces the grid point with an extra space
-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 to specify input files:
-trj[<.xtc/.trr/…>] (traj.xtc) (Optional)
Options to specify output files:
-nbox<vector> (1 1 1)
Number of boxes
-dist<vector> (0 0 0)
Distance between boxes
Random generator seed (0 means generate)
Randomly rotate conformations
-maxrot<vector> (180 180 180)
Maximum random rotation
The program should allow for random displacement of lattice points.