1genbox(1) GROMACS suite, VERSION 4.5 genbox(1)
2
6 genbox - solvates a system
7 VERSION 4.5
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11 genbox -cp protein.gro -cs spc216.gro -ci insert.gro -o out.gro -p
12 topol.top -[no]h -[no]version -nice int -box vector -nmol int -try int
13 -seed int -vdwd real -shell real -maxsol int -[no]vel
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16 Genbox can do one of 3 things:
17 1) Generate a box of solvent. Specify -cs and -box. Or specify -cs and
20 -cp with a structure file with a box, but without atoms.
21 2) Solvate a solute configuration, eg. a protein, in a bath of solvent
24 molecules. Specify -cp (solute) and -cs (solvent). The box specified
25 in the solute coordinate file ( -cp) is used, unless -box is set. If
26 you want the solute to be centered in the box, the program editconf
27 has sophisticated options to change the box dimensions and center the
28 solute. Solvent molecules are removed from the box where the distance
29 between any atom of the solute molecule(s) and any atom of the solvent
30 molecule is less than the sum of the VanderWaals radii of both atoms. A
31 database ( vdwradii.dat) of VanderWaals radii is read by the program,
32 atoms not in the database are assigned a default distance -vdwd. Note
33 that this option will also influence the distances between solvent mol‐
34 ecules if they contain atoms that are not in the database.
35 3) Insert a number ( -nmol) of extra molecules ( -ci) at random posi‐
38 tions. The program iterates until nmol molecules have been inserted
39 in the box. To test whether an insertion is successful the same Vander‐
40 Waals criterium is used as for removal of solvent molecules. When no
41 appropriately sized holes (holes that can hold an extra molecule) are
42 available the program tries for -nmol * -try times before giving up.
43 Increase -try if you have several small holes to fill.
44 The default solvent is Simple Point Charge water (SPC), with coordi‐
47 nates from $GMXLIB/spc216.gro. These coordinates can also be used for
48 other 3-site water models, since a short equibilibration will remove
49 the small differences between the models. Other solvents are also sup‐
50 ported, as well as mixed solvents. The only restriction to solvent
51 types is that a solvent molecule consists of exactly one residue. The
52 residue information in the coordinate files is used, and should there‐
53 fore be more or less consistent. In practice this means that two sub‐
54 sequent solvent molecules in the solvent coordinate file should have
55 different residue number. The box of solute is built by stacking the
56 coordinates read from the coordinate file. This means that these coor‐
57 dinates should be equlibrated in periodic boundary conditions to ensure
58 a good alignment of molecules on the stacking interfaces. The -maxsol
59 option simply adds only the first -maxsol solvent molecules and leaves
60 out the rest would have fit into the box.
61 The program can optionally rotate the solute molecule to align the
64 longest molecule axis along a box edge. This way the amount of solvent
65 molecules necessary is reduced. It should be kept in mind that this
66 only works for short simulations, as eg. an alpha-helical peptide in
67 solution can rotate over 90 degrees, within 500 ps. In general it is
68 therefore better to make a more or less cubic box.
69 Setting -shell larger than zero will place a layer of water of the
72 specified thickness (nm) around the solute. Hint: it is a good idea to
73 put the protein in the center of a box first (using editconf).
74 Finally, genbox will optionally remove lines from your topology file in
77 which a number of solvent molecules is already added, and adds a line
78 with the total number of solvent molecules in your coordinate file.
79
81 -cp protein.gro Input, Opt.
82 Structure file: gro g96 pdb tpr etc.
83 -cs spc216.gro Input, Opt., Lib.
85 Structure file: gro g96 pdb tpr etc.
86 -ci insert.gro Input, Opt.
88 Structure file: gro g96 pdb tpr etc.
89 -o out.gro Output
91 Structure file: gro g96 pdb etc.
92 -p topol.top In/Out, Opt.
94 Topology file
95
98 -[no]hno
99 Print help info and quit
100 -[no]versionno
102 Print version info and quit
103 -nice int 19
105 Set the nicelevel
106 -box vector 0 0 0
108 box size
109 -nmol int 0
111 no of extra molecules to insert
112 -try int 10
114 try inserting -nmol*-try times
115 -seed int 1997
117 random generator seed
118 -vdwd real 0.105
120 default vdwaals distance
121 -shell real 0
123 thickness of optional water layer around solute
124 -maxsol int 0
126 maximum number of solvent molecules to add if they fit in the box. If
127 zero (default) this is ignored
128 -[no]velno
130 keep velocities from input solute and solvent
131
134 - Molecules must be whole in the initial configurations.
135
138 gromacs(7)
139 More information about GROMACS is available at <http://www.gro‐
141 macs.org/>.
142 Thu 26 Aug 2010 genbox(1)