1 .TH genbox 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
3 genbox - solvates a system
8 .BI "\-cp" " protein.gro "
9 .BI "\-cs" " spc216.gro "
10 .BI "\-ci" " insert.gro "
12 .BI "\-p" " topol.top "
14 .BI "\-[no]version" ""
16 .BI "\-box" " vector "
21 .BI "\-shell" " real "
22 .BI "\-maxsol" " int "
25 \&Genbox can do one of 3 things:
28 \&1) Generate a box of solvent. Specify \-cs and \-box. Or specify \-cs and
29 \&\-cp with a structure file with a box, but without atoms.
32 \&2) Solvate a solute configuration, eg. a protein, in a bath of solvent
33 \&molecules. Specify \fB \-cp\fR (solute) and \fB \-cs\fR (solvent).
34 \&The box specified in the solute coordinate file (\fB \-cp\fR) is used,
35 \&unless \fB \-box\fR is set.
36 \&If you want the solute to be centered in the box,
37 \&the program \fB editconf\fR has sophisticated options
38 \&to change the box dimensions and center the solute.
39 \&Solvent molecules are removed from the box where the
40 \&distance between any atom of the solute molecule(s) and any atom of
41 \&the solvent molecule is less than the sum of the VanderWaals radii of
42 \&both atoms. A database (\fB vdwradii.dat\fR) of VanderWaals radii is
43 \&read by the program, atoms not in the database are
44 \&assigned a default distance \fB \-vdwd\fR.
45 \&Note that this option will also influence the distances between
46 \&solvent molecules if they contain atoms that are not in the database.
50 \&3) Insert a number (\fB \-nmol\fR) of extra molecules (\fB \-ci\fR)
51 \&at random positions.
52 \&The program iterates until \fB nmol\fR molecules
53 \&have been inserted in the box. To test whether an insertion is
54 \&successful the same VanderWaals criterium is used as for removal of
55 \&solvent molecules. When no appropriately
56 \&sized holes (holes that can hold an extra molecule) are available the
57 \&program tries for \fB \-nmol\fR * \fB \-try\fR times before giving up.
58 \&Increase \-try if you have several small holes to fill.
61 \&The default solvent is Simple Point Charge water (SPC), with coordinates
62 \&from \fB $GMXLIB/spc216.gro\fR. These coordinates can also be used
63 \&for other 3\-site water models, since a short equibilibration will remove
64 \&the small differences between the models.
65 \&Other solvents are also supported, as well as mixed solvents. The
66 \&only restriction to solvent types is that a solvent molecule consists
67 \&of exactly one residue. The residue information in the coordinate
68 \&files is used, and should therefore be more or less consistent.
69 \&In practice this means that two subsequent solvent molecules in the
70 \&solvent coordinate file should have different residue number.
71 \&The box of solute is built by stacking the coordinates read from
72 \&the coordinate file. This means that these coordinates should be
73 \&equlibrated in periodic boundary conditions to ensure a good
74 \&alignment of molecules on the stacking interfaces.
75 \&The \fB \-maxsol\fR option simply adds only the first \fB \-maxsol\fR
76 \&solvent molecules and leaves out the rest would have fit into the box.
80 \&The program can optionally rotate the solute molecule to align the
81 \&longest molecule axis along a box edge. This way the amount of solvent
82 \&molecules necessary is reduced.
83 \&It should be kept in mind that this only works for
84 \&short simulations, as eg. an alpha\-helical peptide in solution can
85 \&rotate over 90 degrees, within 500 ps. In general it is therefore
86 \&better to make a more or less cubic box.
89 \&Setting \-shell larger than zero will place a layer of water of
90 \&the specified thickness (nm) around the solute. Hint: it is a good
91 \&idea to put the protein in the center of a box first (using editconf).
95 \&Finally, genbox will optionally remove lines from your topology file in
96 \&which a number of solvent molecules is already added, and adds a
97 \&line with the total number of solvent molecules in your coordinate file.
99 .BI "\-cp" " protein.gro"
101 Structure file: gro g96 pdb tpr etc.
103 .BI "\-cs" " spc216.gro"
105 Structure file: gro g96 pdb tpr etc.
107 .BI "\-ci" " insert.gro"
109 Structure file: gro g96 pdb tpr etc.
113 Structure file: gro g96 pdb etc.
115 .BI "\-p" " topol.top"
121 Print help info and quit
123 .BI "\-[no]version" "no "
124 Print version info and quit
126 .BI "\-nice" " int" " 19"
129 .BI "\-box" " vector" " 0 0 0"
132 .BI "\-nmol" " int" " 0"
133 no of extra molecules to insert
135 .BI "\-try" " int" " 10"
136 try inserting \-nmol*\-try times
138 .BI "\-seed" " int" " 1997"
139 random generator seed
141 .BI "\-vdwd" " real" " 0.105 "
142 default vdwaals distance
144 .BI "\-shell" " real" " 0 "
145 thickness of optional water layer around solute
147 .BI "\-maxsol" " int" " 0"
148 maximum number of solvent molecules to add if they fit in the box. If zero (default) this is ignored
150 .BI "\-[no]vel" "no "
151 keep velocities from input solute and solvent
154 \- Molecules must be whole in the initial configurations.
159 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.