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