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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>g_bar</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 g_bar calculates free energy difference estimates through
  18 Bennett's acceptance ratio method.
  19 Input option <tt>-f</tt> expects multiple dhdl files.
  20 Two types of input files are supported:<br>
  21 * Files with only one y-value, for such files it is assumed
  22 that the y-value is dH/dlambda and that the Hamiltonian depends
  23 linearly on lambda. The lambda value of the simulation is inferred
  24 from the subtitle if present, otherwise from a number in the
  25 subdirectory in the file name.
  26 <br>
  27 * Files with more than one y-value. The files should have columns
  28 with dH/dlambda and Delta lambda. The lambda values are inferred
  29 from the legends:
  30 lambda of the simulation from the legend of dH/dlambda
  31 and the foreign lambda's from the legends of Delta H.<p>
  32 The lambda of the simulation is parsed from dhdl.<a href="xvg.html">xvg</a> file's legend
  33 containing the string 'dH', the foreign lambda's from the legend
  34 containing the capitalized letters 'D' and 'H'. The temperature
  35 is parsed from the legend line containing 'T ='.<p>
  36 The free energy estimates are determined using BAR with bisection,
  37 the precision of the output is set with <tt>-prec</tt>.
  38 An error estimate taking into account time correlations
  39 is made by splitting the data into blocks and determining
  40 the free energy differences over those blocks and assuming
  41 the blocks are independent.
  42 The final error estimate is determined from the average variance
  43 over 5 blocks. A range of blocks numbers for error estimation can
  44 be provided with the options <tt>-nbmin</tt> and <tt>-nbmax</tt>.<p>
  45 The results are split in two parts: the last part contains the final
  46 results in kJ/mol, together with the error estimate for each part
  47 and the total. The first part contains detailed free energy
  48 difference estimates and phase space overlap measures in units of
  49 kT (together with their computed error estimate). The printed
  50 values are:<br>
  51 *  lam_A: the lambda values for point A.<br>
  52 *  lam_B: the lambda values for point B.<br>
  53 *     DG: the free energy estimate.<br>
  54 *    s_A: an estimate of the relative entropy of B in A.<br>
  55 *    s_A: an estimate of the relative entropy of A in B.<br>
  56 *  stdev: an estimate expected per-sample standard deviation.<p>
  57 The relative entropy of both states in each other's ensemble can be
  58 interpreted as a measure of phase space overlap:
  59 the relative entropy s_A of the work samples of lambda_B in the
  60 ensemble of lambda_A (and vice versa for s_B), is a
  61 measure of the 'distance' between Boltzmann distributions of
  62 the two states, that goes to zero for identical distributions. See
  63 Wu & Kofke, J. Chem. Phys. 123 084109 (2009) for more information.
  64 <p>
  65 The estimate of the expected per-sample standard deviation, as given
  66 in Bennett's original BAR paper:
  67 Bennett, J. Comp. Phys. 22, p 245 (1976), Eq. 10 gives an estimate
  68 of the quality of sampling (not directly of the actual statistical
  69 error, because it assumes independent samples).<p>
  70 <P>
  71 <H3>Files</H3>
  72 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  73 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  74 <TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    dhdl.xvg</a></tt> </TD><TD> Input, Opt., Mult. </TD><TD> xvgr/xmgr file </TD></TR>
  75 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">     bar.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  76 <TR><TD ALIGN=RIGHT> <b><tt>-oi</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  barint.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  77 <TR><TD ALIGN=RIGHT> <b><tt>-oh</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">histogram.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  78 <TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edr.html">  energy.edr</a></tt> </TD><TD> Input, Opt., Mult. </TD><TD> Energy file </TD></TR>
  79 </TABLE>
  80 <P>
  81 <H3>Other options</H3>
  82 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  83 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  84 <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>
  85 <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>
  86 <TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
  87 <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>
  88 <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>
  89 <TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Begin time for BAR </TD></TD>
  90 <TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1    </tt> </TD><TD> End time for BAR </TD></TD>
  91 <TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1    </tt> </TD><TD> Temperature (K) </TD></TD>
  92 <TR><TD ALIGN=RIGHT> <b><tt>-prec</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>2</tt> </TD><TD> The number of digits after the decimal point </TD></TD>
  93 <TR><TD ALIGN=RIGHT> <b><tt>-nbmin</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>5</tt> </TD><TD> Minimum number of blocks for error estimation </TD></TD>
  94 <TR><TD ALIGN=RIGHT> <b><tt>-nbmax</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>5</tt> </TD><TD> Maximum number of blocks for error estimation </TD></TD>
  95 <TR><TD ALIGN=RIGHT> <b><tt>-nbin</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>100</tt> </TD><TD> Number of bins for histogram output </TD></TD>
  96 </TABLE>
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