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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_sham</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>
  14 <HR>
  15 <H3>Description</H3>
  16 <p>
  17 <tt>g_sham</tt> makes multi-dimensional free-energy, enthalpy and entropy plots.
  18 <tt>g_sham</tt> reads one or more <tt>.<a href="xvg.html">xvg</a></tt> files and analyzes data sets.
  19 The basic purpose of <tt>g_sham</tt> is to plot Gibbs free energy landscapes
  20 (option <tt>-ls</tt>)
  21 by Bolzmann inverting multi-dimensional histograms (option <tt>-lp</tt>),
  22 but it can also
  23 make enthalpy (option <tt>-lsh</tt>) and entropy (option <tt>-lss</tt>)
  24 plots. The histograms can be made for any quantities the user supplies.
  25 A line in the input file may start with a time
  26 (see option <tt>-time</tt>) and any number of <it>y</it>-values may follow.
  27 Multiple sets can also be
  28 read when they are separated by & (option <tt>-n</tt>),
  29 in this case only one <it>y</it>-value is read from each line.
  30 All lines starting with # and @ are skipped.
  31 <p>
  32 Option <tt>-ge</tt> can be used to supply a file with free energies
  33 when the ensemble is not a Boltzmann ensemble, but needs to be biased
  34 by this free energy. One free energy value is required for each
  35 (multi-dimensional) data point in the <tt>-f</tt> input.
  36 <p>
  37 Option <tt>-<a href="ene.html">ene</a></tt> can be used to supply a file with energies.
  38 These energies are used as a weighting function in the single
  39 histogram analysis method by Kumar et al. When temperatures
  40 are supplied (as a second column in the file), an experimental
  41 weighting scheme is applied. In addition the vales
  42 are used for making enthalpy and entropy plots.
  43 <p>
  44 With option <tt>-dim</tt>, dimensions can be gives for distances.
  45 When a distance is 2- or 3-dimensional, the circumference or surface
  46 sampled by two particles increases with increasing distance.
  47 Depending on what one would like to show, one can choose to correct
  48 the histogram and free-energy for this volume effect.
  49 The probability is normalized by r and r^2 for dimensions of 2 and 3,
  50 respectively.
  51 A value of -1 is used to indicate an angle in degrees between two
  52 vectors: a sin(angle) normalization will be applied.
  53 <b>Note</b> that for angles between vectors the inner-product or cosine
  54 is the natural quantity to use, as it will produce bins of the same
  55 volume.
  56 <P>
  57 <H3>Files</H3>
  58 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  59 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  60 <TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   graph.xvg</a></tt> </TD><TD> Input </TD><TD> xvgr/xmgr file </TD></TR>
  61 <TR><TD ALIGN=RIGHT> <b><tt>-ge</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   gibbs.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  62 <TR><TD ALIGN=RIGHT> <b><tt>-ene</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   esham.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  63 <TR><TD ALIGN=RIGHT> <b><tt>-dist</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    ener.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  64 <TR><TD ALIGN=RIGHT> <b><tt>-histo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   edist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  65 <TR><TD ALIGN=RIGHT> <b><tt>-bin</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">  bindex.ndx</a></tt> </TD><TD> Output, Opt. </TD><TD> Index file </TD></TR>
  66 <TR><TD ALIGN=RIGHT> <b><tt>-lp</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">    prob.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
  67 <TR><TD ALIGN=RIGHT> <b><tt>-ls</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">   gibbs.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
  68 <TR><TD ALIGN=RIGHT> <b><tt>-lsh</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">enthalpy.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
  69 <TR><TD ALIGN=RIGHT> <b><tt>-lss</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> entropy.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
  70 <TR><TD ALIGN=RIGHT> <b><tt>-map</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">     map.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
  71 <TR><TD ALIGN=RIGHT> <b><tt>-ls3</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html">  gibbs3.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Protein data bank file </TD></TR>
  72 <TR><TD ALIGN=RIGHT> <b><tt>-mdata</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> mapdata.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  73 <TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html"> shamlog.log</a></tt> </TD><TD> Output, Opt. </TD><TD> Log file </TD></TR>
  74 </TABLE>
  75 <P>
  76 <H3>Other options</H3>
  77 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  78 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  79 <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>
  80 <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>
  81 <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>
  82 <TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
  83 <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>
  84 <TR><TD ALIGN=RIGHT> <b><tt>-[no]time</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Expect a time in the input </TD></TD>
  85 <TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1    </tt> </TD><TD> First time to read from set </TD></TD>
  86 <TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1    </tt> </TD><TD> Last time to read from set </TD></TD>
  87 <TR><TD ALIGN=RIGHT> <b><tt>-ttol</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Tolerance on time in appropriate units (usually ps) </TD></TD>
  88 <TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Read this number of sets separated by lines containing only an ampersand </TD></TD>
  89 <TR><TD ALIGN=RIGHT> <b><tt>-[no]d</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Use the derivative </TD></TD>
  90 <TR><TD ALIGN=RIGHT> <b><tt>-bw</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.1   </tt> </TD><TD> Binwidth for the distribution </TD></TD>
  91 <TR><TD ALIGN=RIGHT> <b><tt>-[no]sham</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Turn off energy weighting even if energies are given </TD></TD>
  92 <TR><TD ALIGN=RIGHT> <b><tt>-tsham</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>298.15</tt> </TD><TD> Temperature for single histogram analysis </TD></TD>
  93 <TR><TD ALIGN=RIGHT> <b><tt>-pmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Minimum probability. Anything lower than this will be set to zero </TD></TD>
  94 <TR><TD ALIGN=RIGHT> <b><tt>-dim</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>1 1 1</tt> </TD><TD> Dimensions for distances, used for volume correction (max 3 values, dimensions &gt; 3 will get the same value as the last) </TD></TD>
  95 <TR><TD ALIGN=RIGHT> <b><tt>-ngrid</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>32 32 32</tt> </TD><TD> Number of bins for energy landscapes (max 3 values, dimensions &gt; 3 will get the same value as the last) </TD></TD>
  96 <TR><TD ALIGN=RIGHT> <b><tt>-xmin</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Minimum for the axes in energy landscape (see above for &gt; 3 dimensions) </TD></TD>
  97 <TR><TD ALIGN=RIGHT> <b><tt>-xmax</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>1 1 1</tt> </TD><TD> Maximum for the axes in energy landscape (see above for &gt; 3 dimensions) </TD></TD>
  98 <TR><TD ALIGN=RIGHT> <b><tt>-pmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Maximum probability in output, default is calculate </TD></TD>
  99 <TR><TD ALIGN=RIGHT> <b><tt>-gmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Maximum free energy in output, default is calculate </TD></TD>
 100 <TR><TD ALIGN=RIGHT> <b><tt>-emin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Minimum enthalpy in output, default is calculate </TD></TD>
 101 <TR><TD ALIGN=RIGHT> <b><tt>-emax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Maximum enthalpy in output, default is calculate </TD></TD>
 102 <TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>25</tt> </TD><TD> Number of levels for energy landscape </TD></TD>
 103 <TR><TD ALIGN=RIGHT> <b><tt>-mname</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Legend label for the custom landscape </TD></TD>
 104 </TABLE>
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