.TH genbox 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
genbox - solvates a system

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3genbox\fP
.BI "\-cp" " protein.gro "
.BI "\-cs" " spc216.gro "
.BI "\-ci" " insert.gro "
.BI "\-o" " out.gro "
.BI "\-p" " topol.top "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-box" " vector "
.BI "\-nmol" " int "
.BI "\-try" " int "
.BI "\-seed" " int "
.BI "\-vdwd" " real "
.BI "\-shell" " real "
.BI "\-maxsol" " int "
.BI "\-[no]vel" ""
.SH DESCRIPTION
\&\fB genbox\fR can do one of 3 things:


\&1) Generate a box of solvent. Specify \fB \-cs\fR and \fB \-box\fR. Or specify \fB \-cs\fR and
\&\fB \-cp\fR 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 \fB \-cp\fR (solute) and \fB \-cs\fR (solvent). 
\&The box specified in the solute coordinate file (\fB \-cp\fR) is used,
\&unless \fB \-box\fR is set.
\&If you want the solute to be centered in the box,
\&the program \fB editconf\fR 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 van der Waals radii of 
\&both atoms. A database (\fB vdwradii.dat\fR) of van der Waals radii is 
\&read by the program, and atoms not in the database are 
\&assigned a default distance \fB \-vdwd\fR.
\&Note that this option will also influence the distances between
\&solvent molecules if they contain atoms that are not in the database.
\&


\&3) Insert a number (\fB \-nmol\fR) of extra molecules (\fB \-ci\fR) 
\&at random positions.
\&The program iterates until \fB nmol\fR molecules
\&have been inserted in the box. To test whether an insertion is 
\&successful the same van der Waals criterium is used as for removal of 
\&solvent molecules. When no appropriately\-sized 
\&holes (holes that can hold an extra molecule) are available, the 
\&program tries for \fB \-nmol\fR * \fB \-try\fR times before giving up. 
\&Increase \fB \-try\fR if you have several small holes to fill.


\&If you need to do more than one of the above operations, it can be
\&best to call \fB genbox\fR separately for each operation, so that
\&you are sure of the order in which the operations occur.


\&The default solvent is Simple Point Charge water (SPC), with coordinates 
\&from \fB $GMXLIB/spc216.gro\fR. 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 supported, 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 therefore be more or less consistent.
\&In practice this means that two subsequent solvent molecules in the 
\&solvent coordinate file should have different residue number.
\&The box of solute is built by stacking the coordinates read from
\&the coordinate file. This means that these coordinates should be 
\&equlibrated in periodic boundary conditions to ensure a good
\&alignment of molecules on the stacking interfaces.
\&The \fB \-maxsol\fR option simply adds only the first \fB \-maxsol\fR
\&solvent molecules and leaves out the rest would have fit into the box.
\&


\&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 \fB \-shell\fR 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 \fB editconf\fR).
\&


\&Finally, \fB genbox\fR 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.
.SH FILES
.BI "\-cp" " protein.gro" 
.B Input, Opt.
 Structure file: gro g96 pdb tpr etc. 

.BI "\-cs" " spc216.gro" 
.B Input, Opt., Lib.
 Structure file: gro g96 pdb tpr etc. 

.BI "\-ci" " insert.gro" 
.B Input, Opt.
 Structure file: gro g96 pdb tpr etc. 

.BI "\-o" " out.gro" 
.B Output
 Structure file: gro g96 pdb etc. 

.BI "\-p" " topol.top" 
.B In/Out, Opt.
 Topology file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-box"  " vector" " 0 0 0" 
 box size

.BI "\-nmol"  " int" " 0" 
 no of extra molecules to insert

.BI "\-try"  " int" " 10" 
 try inserting \fB \-nmol\fR times \fB \-try\fR times

.BI "\-seed"  " int" " 1997" 
 random generator seed

.BI "\-vdwd"  " real" " 0.105 " 
 default vdwaals distance

.BI "\-shell"  " real" " 0     " 
 thickness of optional water layer around solute

.BI "\-maxsol"  " int" " 0" 
 maximum number of solvent molecules to add if they fit in the box. If zero (default) this is ignored

.BI "\-[no]vel"  "no    "
 keep velocities from input solute and solvent

.SH KNOWN PROBLEMS
\- Molecules must be whole in the initial configurations.

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.