1GMX-GENCONF(1)                      GROMACS                     GMX-GENCONF(1)
2
3
4

NAME

6       gmx-genconf - Multiply a conformation in 'random' orientations
7

SYNOPSIS

9          gmx genconf [-f [<.gro/.g96/...>]] [-trj [<.xtc/.trr/...>]]
10                      [-o [<.gro/.g96/...>]] [-nbox <vector>] [-dist <vector>]
11                      [-seed <int>] [-[no]rot] [-maxrot <vector>]
12                      [-[no]renumber]
13

DESCRIPTION

15       gmx  genconf multiplies a given coordinate file by simply stacking them
16       on top of each other, like a small child playing  with  wooden  blocks.
17       The  program  makes a grid of user-defined proportions (-nbox), and in‐
18       terspaces the grid point with an extra space -dist.
19
20       When option -rot is used the program does not check for overlap between
21       molecules  on grid points. It is recommended to make the box in the in‐
22       put file at least as big as the coordinates + van der Waals radius.
23
24       If the optional trajectory file is given, conformations are not  gener‐
25       ated, but read from this file and translated appropriately to build the
26       grid.
27

OPTIONS

29       Options to specify input files:
30
31       -f [<.gro/.g96/...>] (conf.gro)
32              Structure file: gro g96 pdb brk ent esp tpr
33
34       -trj [<.xtc/.trr/...>] (traj.xtc) (Optional)
35              Trajectory: xtc trr cpt gro g96 pdb tng
36
37       Options to specify output files:
38
39       -o [<.gro/.g96/...>] (out.gro)
40              Structure file: gro g96 pdb brk ent esp
41
42       Other options:
43
44       -nbox <vector> (1 1 1)
45              Number of boxes
46
47       -dist <vector> (0 0 0)
48              Distance between boxes
49
50       -seed <int> (0)
51              Random generator seed (0 means generate)
52
53       -[no]rot (no)
54              Randomly rotate conformations
55
56       -maxrot <vector> (180 180 180)
57              Maximum random rotation
58
59       -[no]renumber (yes)
60              Renumber residues
61

KNOWN ISSUES

63       • The program should allow for random displacement of lattice points.
64

SEE ALSO

66       gmx(1)
67
68       More    information    about    GROMACS    is    available    at     <‐
69       http://www.gromacs.org/>.
70

72       2022, GROMACS development team
73
74
75
76
772022.3                           Sep 02, 2022                   GMX-GENCONF(1)
Impressum