1GMX-SOLVATE(1) GROMACS GMX-SOLVATE(1)
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6 gmx-solvate - Solvate a system
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9 gmx solvate [-cp [<.gro/.g96/...>]] [-cs [<.gro/.g96/...>]]
10 [-p [<.top>]] [-o [<.gro/.g96/...>]] [-box <vector>]
11 [-radius <real>] [-scale <real>] [-shell <real>]
12 [-maxsol <int>] [-[no]vel]
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15 gmx solvate can do one of 2 things:
16 1) Generate a box of solvent. Specify -cs and -box. Or specify -cs and
18 -cp with a structure file with a box, but without atoms.
19 2) Solvate a solute configuration, e.g. a protein, in a bath of solvent
21 molecules. Specify -cp (solute) and -cs (solvent). The box specified
22 in the solute coordinate file (-cp) is used, unless -box is set. If
23 you want the solute to be centered in the box, the program gmx editconf
24 has sophisticated options to change the box dimensions and center the
25 solute. Solvent molecules are removed from the box where the distance
26 between any atom of the solute molecule(s) and any atom of the solvent
27 molecule is less than the sum of the scaled van der Waals radii of both
28 atoms. A database (vdwradii.dat) of van der Waals radii is read by the
29 program, and the resulting radii scaled by -scale. If radii are not
30 found in the database, those atoms are assigned the (pre-scaled) dis‐
31 tance -radius. Note that the usefulness of those radii depends on the
32 atom names, and thus varies widely with force field.
33 The default solvent is Simple Point Charge water (SPC), with coordi‐
35 nates from $GMXLIB/spc216.gro. These coordinates can also be used for
36 other 3-site water models, since a short equibilibration will remove
37 the small differences between the models. Other solvents are also sup‐
38 ported, as well as mixed solvents. The only restriction to solvent
39 types is that a solvent molecule consists of exactly one residue. The
40 residue information in the coordinate files is used, and should there‐
41 fore be more or less consistent. In practice this means that two sub‐
42 sequent solvent molecules in the solvent coordinate file should have
43 different residue number. The box of solute is built by stacking the
44 coordinates read from the coordinate file. This means that these coor‐
45 dinates should be equlibrated in periodic boundary conditions to ensure
46 a good alignment of molecules on the stacking interfaces. The -maxsol
47 option simply adds only the first -maxsol solvent molecules and leaves
48 out the rest that would have fitted into the box. This can create a
49 void that can cause problems later. Choose your volume wisely.
50 Setting -shell larger than zero will place a layer of water of the
52 specified thickness (nm) around the solute. Hint: it is a good idea to
53 put the protein in the center of a box first (using gmx editconf).
54 Finally, gmx solvate will optionally remove lines from your topology
56 file in which a number of solvent molecules is already added, and adds
57 a line with the total number of solvent molecules in your coordinate
58 file.
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61 Options to specify input files:
62 -cp [<.gro/.g96/…>] (protein.gro) (Optional)
64 Structure file: gro g96 pdb brk ent esp tpr
65 -cs [<.gro/.g96/…>] (spc216.gro) (Library)
67 Structure file: gro g96 pdb brk ent esp tpr
68 Options to specify input/output files:
70 -p [<.top>] (topol.top) (Optional)
72 Topology file
73 Options to specify output files:
75 -o [<.gro/.g96/…>] (out.gro)
77 Structure file: gro g96 pdb brk ent esp
78 Other options:
80 -box <vector> (0 0 0)
82 Box size (in nm)
83 -radius <real> (0.105)
85 Default van der Waals distance
86 -scale <real> (0.57)
88 Scale factor to multiply Van der Waals radii from the database
89 in share/gromacs/top/vdwradii.dat. The default value of 0.57
90 yields density close to 1000 g/l for proteins in water.
91 -shell <real> (0)
93 Thickness of optional water layer around solute
94 -maxsol <int> (0)
96 Maximum number of solvent molecules to add if they fit in the
97 box. If zero (default) this is ignored
98 -[no]vel (no)
100 Keep velocities from input solute and solvent
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103 · Molecules must be whole in the initial configurations.
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106 gmx(1)
107 More information about GROMACS is available at <‐
109 http://www.gromacs.org/>.
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112 2020, GROMACS development team
1132019.6 Feb 28, 2020 GMX-SOLVATE(1)