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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_lie</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 g_lie computes a free energy estimate based on an energy analysis
  18 from. One needs an energy file with the following components:
  19 Coul (A-B) LJ-SR (A-B) etc.
  20 <P>
  21 <H3>Files</H3>
  22 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  23 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  24 <TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edr.html">    ener.edr</a></tt> </TD><TD> Input </TD><TD> Energy file </TD></TR>
  25 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">     lie.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  26 </TABLE>
  27 <P>
  28 <H3>Other options</H3>
  29 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  30 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  31 <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>
  32 <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>
  33 <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>
  34 <TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
  35 <TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
  36 <TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
  37 <TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
  38 <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>
  39 <TR><TD ALIGN=RIGHT> <b><tt>-Elj</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Lennard-Jones interaction between ligand and solvent </TD></TD>
  40 <TR><TD ALIGN=RIGHT> <b><tt>-Eqq</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Coulomb interaction between ligand and solvent </TD></TD>
  41 <TR><TD ALIGN=RIGHT> <b><tt>-Clj</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.181 </tt> </TD><TD> Factor in the LIE equation for Lennard-Jones component of energy </TD></TD>
  42 <TR><TD ALIGN=RIGHT> <b><tt>-Cqq</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.5   </tt> </TD><TD> Factor in the LIE equation for Coulomb component of energy </TD></TD>
  43 <TR><TD ALIGN=RIGHT> <b><tt>-ligand</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Name of the ligand in the energy file </TD></TD>
  44 </TABLE>
  45 <P>
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  48 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
  49 <font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
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