gmx solvate¶
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, those
atoms are assigned the (pre-scaled) distance -radius.
Note that the usefulness of those radii depends on the atom names,
and thus varies widely with force field.
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:
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.