Provided by: gromacs-data_4.5.5-1_all bug

NAME

       genbox - solvates a system

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

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

DESCRIPTION

        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, e.g. 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
       van der Waals radii of both atoms. A database ( vdwradii.dat) of van der  Waals  radii  is
       read by the program, and atoms not in the database are assigned a default distance  -vdwd.
       Note that this option will also influence the distances between solvent molecules if  they
       contain atoms that are not in the database.

       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  van  der  Waals  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 fill.

       If you need to do more than one of the above operations, it can be best  to  call   genbox
       separately  for  each operation, so that you are sure of the order in which the operations
       occur.

       The  default  solvent  is  Simple  Point  Charge  water  (SPC),  with   coordinates   from
       $GMXLIB/spc216.gro.  These  coordinates  can  also  be used for other 3-site water models,
       since a short equibilibration will remove the small differences between the models.  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  -maxsol option simply adds  only  the  first   -maxsol  solvent
       molecules and leaves out the rest would have fit into the box.

       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  e.g. 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.

FILES

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

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

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

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

       -p topol.top In/Out, Opt.
        Topology file

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version 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 times  -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

       -[no]velno
        keep velocities from input solute and solvent

KNOWN PROBLEMS

       - Molecules must be whole in the initial configurations.

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

                                          Mon 4 Apr 2011                                genbox(1)