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       genbox - solvates a system

       VERSION 4.0.1


       genbox  -cp  protein.gro  -cs  spc216.gro  -ci insert.gro -o out.gro -p -[no]h -nice int -box vector -nmol int  -try  int  -seed  int
       -vdwd real -shell real -maxsol int -[no]vel


       Genbox can do one of 3 things:

       1)  Generate a box of solvent. Specify -cs and -box. Or specify -cs and
       -cp with a structure file with a box, but without atoms.

       2) Solvate a solute configuration, eg. a protein, in a bath of  solvent
       molecules. Specify  -cp (solute) and  -cs (solvent).  The box specified
       in the solute coordinate file ( -cp) is used, unless  -box is set.   If
       you  want  the  solute to be centered in the box, the program  editconf
       has sophisticated options to change the box dimensions and  center  the
       solute.   Solvent molecules are removed from the box where the distance
       between any atom of the solute molecule(s) and any atom of the  solvent
       molecule is less than the sum of the VanderWaals radii of both atoms. A
       database ( vdwradii.dat) of VanderWaals radii is read by  the  program,
       atoms not in the database are assigned a default distance  -vdw.

       3)  Insert  a  number  (  -nmol)  of  extra  molecules ( -ci) at random
       positions.  The  program  iterates  until   nmol  molecules  have  been
       inserted  in  the  box.  To test whether an insertion is successful the
       same VanderWaals criterium is used as for removal of solvent molecules.
       When  no  appropriately  sized  holes  (holes  that  can  hold an extra
       molecule) are available the program tries  for   -nmol  *   -try  times
       before  giving  up.   Increase  -try if you have several small holes to

       The  default  solvent  is  Simple  Point  Charge  water   (SPC),   with
       coordinates   from    $GMXLIB/spc216.gro.   Other   solvents  are  also
       supported, as well as mixed solvents. The only restriction  to  solvent
       types  is  that a solvent molecule consists of exactly one residue. The
       residue information  in  the  coordinate  files  is  used,  and  should
       therefore  be more or less consistent.  In practice this means that two
       subsequent solvent molecules in the solvent coordinate file should have
       different  residue  number.  The box of solute is built by stacking the
       coordinates read from  the  coordinate  file.  This  means  that  these
       coordinates  should  be  equlibrated in periodic boundary conditions to
       ensure a good alignment of molecules on the stacking interfaces.

       The program can optionally rotate the  solute  molecule  to  align  the
       longest  molecule axis along a box edge. This way the amount of solvent
       molecules necessary is reduced.  It should be kept in  mind  that  this
       only  works  for  short simulations, as eg. an alpha-helical peptide in
       solution can rotate over 90 degrees, within 500 ps. In  general  it  is
       therefore better to make a more or less cubic box.

       Setting  -shell  larger  than  zero  will place a layer of water of the
       specified thickness (nm) around the solute. Hint: it is a good idea  to
       put the protein in the center of a box first (using editconf).

       Finally, genbox will optionally remove lines from your topology file in
       which a number of solvent molecules is already added, and adds  a  line
       with the total number of solvent molecules in your coordinate file.


       -cp protein.gro Input, Opt.
        Structure file: gro g96 pdb tpr tpb tpa

       -cs spc216.gro Input, Opt., Lib.
        Structure file: gro g96 pdb tpr tpb tpa

       -ci insert.gro Input, Opt.
        Structure file: gro g96 pdb tpr tpb tpa

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

       -p In/Out, Opt.
        Topology file


        Print help info and quit

       -nice int 19
        Set the nicelevel

       -box vector 0 0 0
        box size

       -nmol int 0
        no of extra molecules to insert

       -try int 10
        try inserting -nmol*-try times

       -seed int 1997
        random generator seed

       -vdwd real 0.105
        default vdwaals distance

       -shell real 0
        thickness of optional water layer around solute

       -maxsol int 0
        maximum  number of solvent molecules to add if they fit in the box. If
       zero (default) this is ignored

        keep velocities from input solute and solvent


       - Molecules must be whole in the initial configurations.



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                                Thu 16 Oct 2008                      genbox(1)