1genconf(1)                GROMACS suite, VERSION 4.5                genconf(1)
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NAME

6       genconf - multiplies a conformation in 'random' orientations
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8       VERSION 4.5
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SYNOPSIS

11       genconf  -f conf.gro -o out.gro -trj traj.xtc -[no]h -[no]version -nice
12       int -nbox vector -dist vector -seed int -[no]rot -[no]shuffle -[no]sort
13       -block int -nmolat int -maxrot vector -[no]renumber
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DESCRIPTION

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

33       -f conf.gro Input
34        Structure file: gro g96 pdb tpr etc.
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36       -o out.gro Output
37        Structure file: gro g96 pdb etc.
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39       -trj traj.xtc Input, Opt.
40        Trajectory: xtc trr trj gro g96 pdb cpt
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OTHER OPTIONS

44       -[no]hno
45        Print help info and quit
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47       -[no]versionno
48        Print version info and quit
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50       -nice int 0
51        Set the nicelevel
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53       -nbox vector 1 1 1
54        Number of boxes
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56       -dist vector 0 0 0
57        Distance between boxes
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59       -seed int 0
60        Random generator seed, if 0 generated from the time
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62       -[no]rotno
63        Randomly rotate conformations
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65       -[no]shuffleno
66        Random shuffling of molecules
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68       -[no]sortno
69        Sort molecules on X coord
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71       -block int 1
72        Divide the box in blocks on this number of cpus
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74       -nmolat int 3
75        Number of atoms per molecule, assumed to start from 0. If you set this
76       wrong, it will screw up your system!
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78       -maxrot vector 180 180 180
79        Maximum random rotation
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81       -[no]renumberyes
82        Renumber residues
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KNOWN PROBLEMS

86       - The program should allow for random displacement of lattice points.
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SEE ALSO

90       gromacs(7)
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92       More  information  about  GROMACS  is  available  at   <http://www.gro‐
93       macs.org/>.
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97                                Thu 26 Aug 2010                     genconf(1)
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