xgas(1X)xgas(1X)NAME
xgas - animated simulation of an ideal gas
SYNOPSIS
xgas [-option...]
OPTIONS
This is a toolkit program; all the usual toolkit options are available. Sets the autoStart resource. Sets the timeStepSize resource.
Sets the delay resource. Sets the randomBounce resource. Sets the equilibrium resource. Sets the maxMolecules resource. Sets the fore-
ground. Sets the background.
DESCRIPTION
xgas is a physical simulation of an ideal gas in a heated box. Gas molecules move around the box with velocities dependent on their temper-
ature. A chamber consisting of two boxes contains the gas molecules; the temperature of each box can be independently controlled by a
scrollbar. When gas molecules collide with the walls, their temperature approaches that of the box.
Use mouse button 1 to create molecules one at a time at the cursor position. Use mouse button 2 to create the maximum number of molecules
at the cursor position.
RESOURCES
The xgas program uses the following X resources: Starts the simulation automatically. Good for canned demos. Specifies the simulated time
duration in microseconds for each cycle of computation. Specifies the real time interval between timestep computations. In each wall col-
lision, a molecule bounces elastically (angle of incidence = angle of reflection). A component of randomness is added to this angle. Ran-
domBounce varies from 0.0 (no randomness) to 1.0 (completely random angle of incidence). During each wall collision, a molecule's kinetic
energy approaches that corresponding to the temperature of the wall. If equilibrium is 1.0, the molecule reaches the wall temperature imme-
diately. For values between 1.0 and 0.0, the molecule approaches the temperature of the wall more slowly. Specifies the maximum number of
molecules in the simulation.
BUGS
When the chamber is resized, molecules should be rearranged appropriately. Instead, the molecule arrays are reinitialized.
SEE ALSO X(1X), xwd(1X)AUTHOR
Larry Medwin
xgas(1X)
Check Out this Related Man Page
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)