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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 4.6<br>
  13 Sat 19 Jan 2013</B></td></tr></TABLE>
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  15 <H3>Description</H3>
  16 <p>
  17 <tt>genbox</tt> can do one of 3 things:<p>
  18 1) Generate a box of solvent. Specify <tt>-cs</tt> and <tt>-box</tt>. Or specify <tt>-cs</tt> and
  19 <tt>-cp</tt> with a structure file with a box, but without atoms.<p>
  20 2) Solvate a solute configuration, e.g. 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 van der Waals radii of
  30 both atoms. A database (<tt>vdwradii.<a href="dat.html">dat</a></tt>) of van der Waals radii is
  31 read by the program, and 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 van der Waals criterium is used as for removal of
  41 solvent molecules. When no appropriately-sized
  42 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 <tt>-try</tt> if you have several small holes to fill.<p>
  45 If you need to do more than one of the above operations, it can be
  46 best to call <tt>genbox</tt> separately for each operation, so that
  47 you are sure of the order in which the operations occur.<p>
  48 The default solvent is Simple Point Charge water (SPC), with coordinates
  49 from <tt>$GMXLIB/spc216.<a href="gro.html">gro</a></tt>. These coordinates can also be used
  50 for other 3-site water models, since a short equibilibration will remove
  51 the small differences between the models.
  52 Other solvents are also supported, as well as mixed solvents. The
  53 only restriction to solvent types is that a solvent molecule consists
  54 of exactly one residue. The residue information in the coordinate
  55 files is used, and should therefore be more or less consistent.
  56 In practice this means that two subsequent solvent molecules in the
  57 solvent coordinate file should have different residue number.
  58 The box of solute is built by stacking the coordinates read from
  59 the coordinate file. This means that these coordinates should be
  60 equlibrated in periodic boundary conditions to ensure a good
  61 alignment of molecules on the stacking interfaces.
  62 The <tt>-maxsol</tt> option simply adds only the first <tt>-maxsol</tt>
  63 solvent molecules and leaves out the rest that would have fitted
  64 into the box. This can create a void that can cause problems later.
  65 Choose your volume wisely.<p>
  66 The program can optionally rotate the solute molecule to align the
  67 longest molecule axis along a box edge. This way the amount of solvent
  68 molecules necessary is reduced.
  69 It should be kept in mind that this only works for
  70 short simulations, as e.g. an alpha-helical peptide in solution can
  71 rotate over 90 degrees, within 500 ps. In general it is therefore
  72 better to make a more or less cubic box.<p>
  73 Setting <tt>-shell</tt> larger than zero will place a layer of water of
  74 the specified thickness (nm) around the solute. Hint: it is a good
  75 idea to put the protein in the center of a box first (using <tt><a href="editconf.html">editconf</a></tt>).
  76 <p>
  77 Finally, <tt>genbox</tt> will optionally remove lines from your topology file in
  78 which a number of solvent molecules is already added, and adds a
  79 line with the total number of solvent molecules in your coordinate file.
  80 <P>
  81 <H3>Files</H3>
  82 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  83 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  84 <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>
  85 <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>
  86 <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>
  87 <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>
  88 <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>
  89 </TABLE>
  90 <P>
  91 <H3>Other options</H3>
  92 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  93 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  94 <TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print help info and quit </TD></TD>
  95 <TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print version info and quit </TD></TD>
  96 <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>
  97 <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>
  98 <TR><TD ALIGN=RIGHT> <b><tt>-nmol</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of extra molecules to insert </TD></TD>
  99 <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 <tt>-nmol</tt> times <tt>-try</tt> times </TD></TD>
 100 <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>
 101 <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 van der Waals distance </TD></TD>
 102 <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>
 103 <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>
 104 <TR><TD ALIGN=RIGHT> <b><tt>-[no]vel</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Keep velocities from input solute and solvent </TD></TD>
 105 </TABLE>
 106 <P>
 107 <H3>Known problems</H3>
 108 <UL>
 109 <LI>Molecules must be whole in the initial configurations.
 110 </UL>
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