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       genconf - multiplies a conformation in ’random’ orientations

       VERSION 4.0.1


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


       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

       If  the  optional  trajectory  file  is  given,  conformations  are not
       generated, but read from this  file  and  translated  appropriately  to
       build the grid.


       -f conf.gro Input
        Structure file: gro g96 pdb tpr tpb tpa

       -o out.gro Output
        Structure file: gro g96 pdb

       -trj traj.xtc Input, Opt.
        Trajectory: xtc trr trj gro g96 pdb cpt


        Print help info and quit

       -nice int 0
        Set the nicelevel

       -nbox vector 1 1 1
        Number of boxes

       -dist vector 0 0 0
        Distance between boxes

       -seed int 0
        Random generator seed, if 0 generated from the time

        Randomly rotate conformations

        Random shuffling of molecules

        Sort molecules on X coord

       -block int 1
        Divide the box in blocks on this number of cpus

       -nmolat int 3
        Number of atoms per molecule, assumed to start from 0. If you set this
       wrong, it will screw up your system!

       -maxrot vector 90 90 90
        Maximum random rotation

        Renumber residues


       - The program should allow for random displacement off lattice  points.



       More      information     about     GROMACS     is     available     at

                                Thu 16 Oct 2008                     genconf(1)