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  10 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>genbox</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
  12 </TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
  13 Thu 26 Aug 2010</B></td></tr></TABLE>
  14 <HR>
  15 <H3>Description</H3>
  16 <p>
  17 Genbox can do one of 3 things:<p>
  18 1) Generate a box of solvent. Specify -cs and -box. Or specify -cs and
  19 -cp with a structure file with a box, but without atoms.<p>
  20 2) Solvate a solute configuration, eg. a protein, in a bath of solvent
  21 molecules. Specify <tt>-cp</tt> (solute) and <tt>-cs</tt> (solvent).
  22 The box specified in the solute coordinate file (<tt>-cp</tt>) is used,
  23 unless <tt>-box</tt> is set.
  24 If you want the solute to be centered in the box,
  25 the program <tt><a href="editconf.html">editconf</a></tt> has sophisticated options
  26 to change the box dimensions and center the solute.
  27 Solvent molecules are removed from the box where the
  28 distance between any atom of the solute molecule(s) and any atom of
  29 the solvent molecule is less than the sum of the VanderWaals radii of
  30 both atoms. A database (<tt>vdwradii.<a href="dat.html">dat</a></tt>) of VanderWaals radii is
  31 read by the program, atoms not in the database are
  32 assigned a default distance <tt>-vdwd</tt>.
  33 Note that this option will also influence the distances between
  34 solvent molecules if they contain atoms that are not in the database.
  35 <p>
  36 3) Insert a number (<tt>-nmol</tt>) of extra molecules (<tt>-ci</tt>)
  37 at random positions.
  38 The program iterates until <tt>nmol</tt> molecules
  39 have been inserted in the box. To test whether an insertion is
  40 successful the same VanderWaals criterium is used as for removal of
  41 solvent molecules. When no appropriately
  42 sized holes (holes that can hold an extra molecule) are available the
  43 program tries for <tt>-nmol</tt> * <tt>-try</tt> times before giving up.
  44 Increase -try if you have several small holes to fill.<p>
  45 The default solvent is Simple Point Charge water (SPC), with coordinates
  46 from <tt>$GMXLIB/spc216.<a href="gro.html">gro</a></tt>. These coordinates can also be used
  47 for other 3-site water models, since a short equibilibration will remove
  48 the small differences between the models.
  49 Other solvents are also supported, as well as mixed solvents. The
  50 only restriction to solvent types is that a solvent molecule consists
  51 of exactly one residue. The residue information in the coordinate
  52 files is used, and should therefore be more or less consistent.
  53 In practice this means that two subsequent solvent molecules in the
  54 solvent coordinate file should have different residue number.
  55 The box of solute is built by stacking the coordinates read from
  56 the coordinate file. This means that these coordinates should be
  57 equlibrated in periodic boundary conditions to ensure a good
  58 alignment of molecules on the stacking interfaces.
  59 The <tt>-maxsol</tt> option simply adds only the first <tt>-maxsol</tt>
  60 solvent molecules and leaves out the rest would have fit into the box.
  61 <p>
  62 The program can optionally rotate the solute molecule to align the
  63 longest molecule axis along a box edge. This way the amount of solvent
  64 molecules necessary is reduced.
  65 It should be kept in mind that this only works for
  66 short simulations, as eg. an alpha-helical peptide in solution can
  67 rotate over 90 degrees, within 500 ps. In general it is therefore
  68 better to make a more or less cubic box.<p>
  69 Setting -shell larger than zero will place a layer of water of
  70 the specified thickness (nm) around the solute. Hint: it is a good
  71 idea to put the protein in the center of a box first (using <a href="editconf.html">editconf</a>).
  72 <p>
  73 Finally, genbox will optionally remove lines from your topology file in
  74 which a number of solvent molecules is already added, and adds a
  75 line with the total number of solvent molecules in your coordinate file.
  76 <P>
  77 <H3>Files</H3>
  78 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  79 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  80 <TR><TD ALIGN=RIGHT> <b><tt>-cp</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> protein.gro</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> etc. </TD></TR>
  81 <TR><TD ALIGN=RIGHT> <b><tt>-cs</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">  spc216.gro</a></tt> </TD><TD> Input, Opt., Lib. </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> etc. </TD></TR>
  82 <TR><TD ALIGN=RIGHT> <b><tt>-ci</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">  insert.gro</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> etc. </TD></TR>
  83 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">     out.gro</a></tt> </TD><TD> Output </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> etc. </TD></TR>
  84 <TR><TD ALIGN=RIGHT> <b><tt>-p</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="top.html">   topol.top</a></tt> </TD><TD> In/Out, Opt. </TD><TD> Topology file </TD></TR>
  85 </TABLE>
  86 <P>
  87 <H3>Other options</H3>
  88 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  89 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  90 <TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print help info and quit </TD></TD>
  91 <TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print version info and quit </TD></TD>
  92 <TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
  93 <TR><TD ALIGN=RIGHT> <b><tt>-box</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> box size </TD></TD>
  94 <TR><TD ALIGN=RIGHT> <b><tt>-nmol</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> no of extra molecules to insert </TD></TD>
  95 <TR><TD ALIGN=RIGHT> <b><tt>-try</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>10</tt> </TD><TD> try inserting -nmol*-try times </TD></TD>
  96 <TR><TD ALIGN=RIGHT> <b><tt>-seed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1997</tt> </TD><TD> random generator seed </TD></TD>
  97 <TR><TD ALIGN=RIGHT> <b><tt>-vdwd</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.105 </tt> </TD><TD> default vdwaals distance </TD></TD>
  98 <TR><TD ALIGN=RIGHT> <b><tt>-shell</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> thickness of optional water layer around solute </TD></TD>
  99 <TR><TD ALIGN=RIGHT> <b><tt>-maxsol</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> maximum number of solvent molecules to add if they fit in the box. If zero (default) this is ignored </TD></TD>
 100 <TR><TD ALIGN=RIGHT> <b><tt>-[no]vel</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> keep velocities from input solute and solvent </TD></TD>
 101 </TABLE>
 102 <P>
 103 <H3>Known problems</H3>
 104 <UL>
 105 <LI>Molecules must be whole in the initial configurations.
 106 </UL>
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