gmx-solvate(1) GROMACS Manual gmx-solvate(1)NAMEgmx-solvate - Solvate a system
SYNOPSIS
gmx solvate [-cp [<.gro/.g96/...>]] [-cs [<.gro/.g96/...>]]
[-o [<.gro/.g96/...>]] [-p [<.top>]] [-nice <int>]
[-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) dis‐
tance -radius.
The default solvent is Simple Point Charge water (SPC), with coordi‐
nates 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 sup‐
ported, 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 there‐
fore be more or less consistent. In practice this means that two subse‐
quent solvent molecules in the solvent coordinate file should have dif‐
ferent residue number. The box of solute is built by stacking the coor‐
dinates read from the coordinate file. This means that these coordi‐
nates 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.
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 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 and output files:
-cp [<.gro/.g96/...>] (protein.gro) (Input, Optional)
Structure file: gro g96 pdb brk ent esp tpr tpb tpa
-cs [<.gro/.g96/...>] (spc216.gro) (Input, Library)
Structure file: gro g96 pdb brk ent esp tpr tpb tpa
-o [<.gro/.g96/...>] (out.gro) (Output)
Structure file: gro g96 pdb brk ent esp
-p [<.top>] (topol.top) (Input/Output, Optional)
Topology file
Other options:
-nice <int> (19)
Set the nicelevel
-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 den‐
sity 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.
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-solvate(1)
