genbox(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					 genbox(1)

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 spec-
       ified  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  giv-
       ing 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 sub-
       sequent 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)