Ubuntu Manpage: genbox - solvates a system

Provided by: gromacs-data_4.6.5-1build1_all

NAME

       genbox - solvates a system

       VERSION 4.6.5

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 that would have fitted into the box. This can create a
void that can cause problems later. Choose your volume wisely.

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
        Number 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 van der Waals 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