1 .TH genbox 1 "Fri 19 Apr 2013" "" "GROMACS suite, VERSION 4.5.7"
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 \&\fB genbox\fR can do one of 3 things:
28 \&1) Generate a box of solvent. Specify \fB \-cs\fR and \fB \-box\fR. Or specify \fB \-cs\fR and
29 \&\fB \-cp\fR with a structure file with a box, but without atoms.
32 \&2) Solvate a solute configuration, e.g. 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 van der Waals radii of
42 \&both atoms. A database (\fB vdwradii.dat\fR) of van der Waals radii is
43 \&read by the program, and 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 van der Waals criterium is used as for removal of
55 \&solvent molecules. When no appropriately\-sized
56 \&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 \fB \-try\fR if you have several small holes to fill.
61 \&If you need to do more than one of the above operations, it can be
62 \&best to call \fB genbox\fR separately for each operation, so that
63 \&you are sure of the order in which the operations occur.
66 \&The default solvent is Simple Point Charge water (SPC), with coordinates
67 \&from \fB $GMXLIB/spc216.gro\fR. These coordinates can also be used
68 \&for other 3\-site water models, since a short equibilibration will remove
69 \&the small differences between the models.
70 \&Other solvents are also supported, as well as mixed solvents. The
71 \&only restriction to solvent types is that a solvent molecule consists
72 \&of exactly one residue. The residue information in the coordinate
73 \&files is used, and should therefore be more or less consistent.
74 \&In practice this means that two subsequent solvent molecules in the
75 \&solvent coordinate file should have different residue number.
76 \&The box of solute is built by stacking the coordinates read from
77 \&the coordinate file. This means that these coordinates should be
78 \&equlibrated in periodic boundary conditions to ensure a good
79 \&alignment of molecules on the stacking interfaces.
80 \&The \fB \-maxsol\fR option simply adds only the first \fB \-maxsol\fR
81 \&solvent molecules and leaves out the rest would have fit into the box.
85 \&The program can optionally rotate the solute molecule to align the
86 \&longest molecule axis along a box edge. This way the amount of solvent
87 \&molecules necessary is reduced.
88 \&It should be kept in mind that this only works for
89 \&short simulations, as e.g. an alpha\-helical peptide in solution can
90 \&rotate over 90 degrees, within 500 ps. In general it is therefore
91 \&better to make a more or less cubic box.
94 \&Setting \fB \-shell\fR larger than zero will place a layer of water of
95 \&the specified thickness (nm) around the solute. Hint: it is a good
96 \&idea to put the protein in the center of a box first (using \fB editconf\fR).
100 \&Finally, \fB genbox\fR will optionally remove lines from your topology file in
101 \&which a number of solvent molecules is already added, and adds a
102 \&line with the total number of solvent molecules in your coordinate file.
104 .BI "\-cp" " protein.gro"
106 Structure file: gro g96 pdb tpr etc.
108 .BI "\-cs" " spc216.gro"
110 Structure file: gro g96 pdb tpr etc.
112 .BI "\-ci" " insert.gro"
114 Structure file: gro g96 pdb tpr etc.
118 Structure file: gro g96 pdb etc.
120 .BI "\-p" " topol.top"
126 Print help info and quit
128 .BI "\-[no]version" "no "
129 Print version info and quit
131 .BI "\-nice" " int" " 19"
134 .BI "\-box" " vector" " 0 0 0"
137 .BI "\-nmol" " int" " 0"
138 Number of extra molecules to insert
140 .BI "\-try" " int" " 10"
141 Try inserting \fB \-nmol\fR times \fB \-try\fR times
143 .BI "\-seed" " int" " 1997"
144 Random generator seed
146 .BI "\-vdwd" " real" " 0.105 "
147 Default van der Waals distance
149 .BI "\-shell" " real" " 0 "
150 Thickness of optional water layer around solute
152 .BI "\-maxsol" " int" " 0"
153 Maximum number of solvent molecules to add if they fit in the box. If zero (default) this is ignored
155 .BI "\-[no]vel" "no "
156 Keep velocities from input solute and solvent
159 \- Molecules must be whole in the initial configurations.
164 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.