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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>genion</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>
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  15 <H3>Description</H3>
  16 <p>
  17 genion replaces solvent molecules by monoatomic ions at
  18 the position of the first atoms with the most favorable electrostatic
  19 potential or at random. The potential is calculated on all atoms, using
  20 normal GROMACS particle based methods (in contrast to other methods
  21 based on solving the Poisson-Boltzmann equation).
  22 The potential is recalculated after every ion insertion.
  23 If specified in the run input file, a reaction field, shift function
  24 or user function can be used. For the user function a table file
  25 can be specified with the option <tt>-table</tt>.
  26 The group of solvent molecules should be continuous and all molecules
  27 should have the same number of atoms.
  28 The user should add the ion molecules to the topology file or use
  29 the <tt>-p</tt> option to automatically modify the topology.<p>
  30 The ion molecule type, residue and atom names in all force fields
  31 are the capitalized element names without sign. Ions which can have
  32 multiple charge states get the multiplicilty added, without sign,
  33 for the uncommon states only.<p>
  34 With the option <tt>-pot</tt> the potential can be written as B-factors
  35 in a <a href="pdb.html">pdb</a> file (for visualisation using e.g. rasmol).
  36 The unit of the potential is 1000 kJ/(mol e), the scaling be changed
  37 with the <tt>-scale</tt> option.<p>
  38 For larger ions, e.g. sulfate we recommended to use <a href="genbox.html">genbox</a>.
  39 <P>
  40 <H3>Files</H3>
  41 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  42 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  43 <TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
  44 <TR><TD ALIGN=RIGHT> <b><tt>-table</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   table.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  45 <TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">   index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
  46 <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>
  47 <TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html">  genion.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
  48 <TR><TD ALIGN=RIGHT> <b><tt>-pot</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html">     pot.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Protein data bank file </TD></TR>
  49 <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>
  50 </TABLE>
  51 <P>
  52 <H3>Other options</H3>
  53 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  54 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  55 <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>
  56 <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>
  57 <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>
  58 <TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
  59 <TR><TD ALIGN=RIGHT> <b><tt>-np</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of positive ions </TD></TD>
  60 <TR><TD ALIGN=RIGHT> <b><tt>-pname</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>NA</tt> </TD><TD> Name of the positive ion </TD></TD>
  61 <TR><TD ALIGN=RIGHT> <b><tt>-pq</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Charge of the positive ion </TD></TD>
  62 <TR><TD ALIGN=RIGHT> <b><tt>-nn</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of negative ions </TD></TD>
  63 <TR><TD ALIGN=RIGHT> <b><tt>-nname</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>CL</tt> </TD><TD> Name of the negative ion </TD></TD>
  64 <TR><TD ALIGN=RIGHT> <b><tt>-nq</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Charge of the negative ion </TD></TD>
  65 <TR><TD ALIGN=RIGHT> <b><tt>-rmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.6   </tt> </TD><TD> Minimum distance between ions </TD></TD>
  66 <TR><TD ALIGN=RIGHT> <b><tt>-[no]random</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Use random placement of ions instead of based on potential. The rmin option should still work </TD></TD>
  67 <TR><TD ALIGN=RIGHT> <b><tt>-seed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1993</tt> </TD><TD> Seed for random number generator </TD></TD>
  68 <TR><TD ALIGN=RIGHT> <b><tt>-scale</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.001 </tt> </TD><TD> Scaling factor for the potential for -pot </TD></TD>
  69 <TR><TD ALIGN=RIGHT> <b><tt>-conc</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration as computed from the volume of the cell in the input <a href="tpr.html">tpr</a> file. Overrides the -np and  nn options. </TD></TD>
  70 <TR><TD ALIGN=RIGHT> <b><tt>-[no]neutral</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> This option will add enough ions to neutralize the system. In combination with the concentration option a neutral system at a given salt concentration will be generated. </TD></TD>
  71 </TABLE>
  72 <P>
  73 <H3>Known problems</H3>
  74 <UL>
  75 <LI>Calculation of the potential is not reliable, therefore the <tt>-random</tt> option is now turned on by default.
  76 <LI>If you specify a salt concentration existing ions are not taken into account. In effect you therefore specify the amount of salt to be added.
  77 </UL>
  78 <P>
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