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GMX-GENCONF(1) GROMACS GMX-GENCONF(1) 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] [-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 in- terspaces 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 in- put file at least as big as the coordinates + van der Waals radius. If the optional trajectory file is given, conformations are not gener- ated, 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 (0 means generate) -[no]rot (no) Randomly rotate conformations -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 2025, GROMACS development team 2025.0 Feb 10, 2025 GMX-GENCONF(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | KNOWN ISSUES | SEE ALSO | COPYRIGHT
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