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

6       gmx-genconf - Multiply a conformation in 'random' orientations
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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]
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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
18       interspaces the grid point with an extra space -dist.
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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
22       input file at least as big as the coordinates + van der Waals radius.
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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.
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OPTIONS

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

63       · The program should allow for random displacement of lattice points.
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SEE ALSO

66       gmx(1)
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68       More    information    about    GROMACS    is    available    at     <‐
69       http://www.gromacs.org/>.
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72       2019, GROMACS development team
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772019.4                           Oct 02, 2019                   GMX-GENCONF(1)
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