NAME
genbox - solvates a system
VERSION 4.0.1
SYNOPSIS
genbox -cp protein.gro -cs spc216.gro -ci insert.gro -o out.gro -p
topol.top -[no]h -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, 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
fill.
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.
FILES
-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 topol.top In/Out, Opt.
Topology file
OTHER OPTIONS
-[no]hno
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
-[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/>.
Thu 16 Oct 2008 genbox(1)