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/>.