This is the command gmx-solvate that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
gmx-solvate - Solvate a system
SYNOPSIS
gmx solvate [-cp [<.gro/.g96/...>]] [-cs [<.gro/.g96/...>]]
[-p [<.top>]] [-o [<.gro/.g96/...>]] [-box <vector>]
[-radius <real>] [-scale <real>] [-shell <real>]
[-maxsol <int>] [-[no]vel]
DESCRIPTION
gmx solvate can do one of 2 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
gmx 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 scaled
van der Waals radii of both atoms. A database (vdwradii.dat) of van der Waals radii is
read by the program, and the resulting radii scaled by -scale. If radii are not found in
the database, thoseatoms are assigned the (pre-scaled) distance -radius.
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.
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 gmx editconf).
Finally, gmx solvate 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.
OPTIONS
Options to specify input files:
-cp [<.gro/.g96/...>] (protein.gro) (Optional)
Structure file: gro g96 pdb brk ent esp tpr
-cs [<.gro/.g96/...>] (spc216.gro) (Library)
Structure file: gro g96 pdb brk ent esp tpr
Options to specify input/output files:
-p [<.top>] (topol.top) (Optional)
Topology file
Options to specify output files:
-o [<.gro/.g96/...>] (out.gro)
Structure file: gro g96 pdb brk ent esp
Other options:
-box <vector> (0 0 0)
Box size (in nm)
-radius <real> (0.105)
Default van der Waals distance
-scale <real> (0.57)
Scale factor to multiply Van der Waals radii from the database in
share/gromacs/top/vdwradii.dat. The default value of 0.57 yields density close to
1000 g/l for proteins in water.
-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]vel (no)
Keep velocities from input solute and solvent
KNOWN ISSUES
· Molecules must be whole in the initial configurations.
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