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GMX-GENCONF(1) GROMACS GMX-GENCONF(1)

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

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 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 to specify input files:

Structure file: gro g96 pdb brk ent esp tpr
Trajectory: xtc trr cpt gro g96 pdb tng

Options to specify output files:

Structure file: gro g96 pdb brk ent esp

Other options:

Number of boxes
Distance between boxes
Random generator seed (0 means generate)
-[no]rot (no)
Randomly rotate conformations
Maximum random rotation
-[no]renumber (yes)
Renumber residues

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

gmx(1)

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2019, GROMACS development team

February 15, 2019 2019.1