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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_energy</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_energy extracts energy components or distance restraint
  18 data from an energy file. The user is prompted to interactively
  19 select the energy terms she wants.<p>
  20 Average, RMSD and drift are calculated with full precision from the
  21 simulation (see printed manual). Drift is calculated by performing
  22 a LSQ fit of the data to a straight line. The reported total drift
  23 is the difference of the fit at the first and last point.
  24 An error estimate of the average is given based on a block averages
  25 over 5 blocks using the full precision averages. The error estimate
  26 can be performed over multiple block lengths with the options
  27 <tt>-nbmin</tt> and <tt>-nbmax</tt>.
  28 Note that in most cases the energy files contains averages over all
  29 MD steps, or over many more points than the number of frames in
  30 energy file. This makes the g_energy statistics output more accurate
  31 than the <a href="xvg.html">xvg</a> output. When exact averages are not present in the energy
  32 file the statistics mentioned above is simply over the single, per-frame
  33 energy values.<p>
  34 The term fluctuation gives the RMSD around the LSQ fit.<p>
  35 Some fluctuation-dependent properties can be calculated provided
  36 the correct energy terms are selected. The following properties
  37 will be computed:<br>
  38 Property                        Energy terms needed<br>
  39 ---------------------------------------------------<br>
  40 Heat capacity Cp (NPT sims):    Enthalpy, Temp     <br>
  41 Heat capacity Cv (NVT sims):    Etot, Temp         <br>
  42 Thermal expansion coeff. (NPT): Enthalpy, Vol, Temp<br>
  43 Isothermal compressibility:     Vol, Temp          <br>
  44 Adiabatic bulk modulus:         Vol, Temp          <br>
  45 ---------------------------------------------------<br>
  46 You always need to set the number of molecules <tt>-nmol</tt>, and,
  47 if you used constraints in your simulations you will need to give
  48 the number of constraints per molecule <tt>-nconstr</tt> in order to
  49 correct for this: (nconstr/2) kB is subtracted from the heat
  50 capacity in this case. For instance in the case of rigid water
  51 you need to give the value 3 to this option.<p>
  52 When the <tt>-viol</tt> option is set, the time averaged
  53 violations are plotted and the running time-averaged and
  54 instantaneous sum of violations are recalculated. Additionally
  55 running time-averaged and instantaneous distances between
  56 selected pairs can be plotted with the <tt>-pairs</tt> option.<p>
  57 Options <tt>-ora</tt>, <tt>-ort</tt>, <tt>-oda</tt>, <tt>-odr</tt> and
  58 <tt>-odt</tt> are used for analyzing orientation restraint data.
  59 The first two options plot the orientation, the last three the
  60 deviations of the orientations from the experimental values.
  61 The options that end on an 'a' plot the average over time
  62 as a function of restraint. The options that end on a 't'
  63 prompt the user for restraint label numbers and plot the data
  64 as a function of time. Option <tt>-odr</tt> plots the RMS
  65 deviation as a function of restraint.
  66 When the run used time or ensemble averaged orientation restraints,
  67 option <tt>-orinst</tt> can be used to analyse the instantaneous,
  68 not ensemble-averaged orientations and deviations instead of
  69 the time and ensemble averages.<p>
  70 Option <tt>-oten</tt> plots the eigenvalues of the molecular order
  71 tensor for each orientation restraint experiment. With option
  72 <tt>-ovec</tt> also the eigenvectors are plotted.<p>
  73 With <tt>-fee</tt> an estimate is calculated for the free-energy
  74 difference with an ideal gas state: <br>
  75   Delta A = A(N,V,T) - A_idgas(N,V,T) = kT ln &lt; e^(Upot/kT) &gt;<br>
  76   Delta G = G(N,p,T) - G_idgas(N,p,T) = kT ln &lt; e^(Upot/kT) &gt;<br>
  77 where k is Boltzmann's constant, T is set by <tt>-fetemp</tt> and
  78 the average is over the ensemble (or time in a trajectory).
  79 Note that this is in principle
  80 only correct when averaging over the whole (Boltzmann) ensemble
  81 and using the potential energy. This also allows for an entropy
  82 estimate using:<br>
  83   Delta S(N,V,T) = S(N,V,T) - S_idgas(N,V,T) = (&lt;Upot&gt; - Delta A)/T<br>
  84   Delta S(N,p,T) = S(N,p,T) - S_idgas(N,p,T) = (&lt;Upot&gt; + pV - Delta G)/T
  85 <p>
  86 When a second energy file is specified (<tt>-f2</tt>), a free energy
  87 difference is calculated dF = -kT ln &lt; e ^ -(EB-EA)/kT &gt;A ,
  88 where EA and EB are the energies from the first and second energy
  89 files, and the average is over the ensemble A. <b>NOTE</b> that
  90 the energies must both be calculated from the same trajectory.
  91 <P>
  92 <H3>Files</H3>
  93 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  94 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  95 <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>
  96 <TR><TD ALIGN=RIGHT> <b><tt>-f2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edr.html">    ener.edr</a></tt> </TD><TD> Input, Opt. </TD><TD> Energy file </TD></TR>
  97 <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, Opt. </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>
  98 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  energy.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  99 <TR><TD ALIGN=RIGHT> <b><tt>-viol</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">violaver.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 100 <TR><TD ALIGN=RIGHT> <b><tt>-pairs</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   pairs.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 101 <TR><TD ALIGN=RIGHT> <b><tt>-ora</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> orienta.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 102 <TR><TD ALIGN=RIGHT> <b><tt>-ort</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> orientt.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 103 <TR><TD ALIGN=RIGHT> <b><tt>-oda</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> orideva.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 104 <TR><TD ALIGN=RIGHT> <b><tt>-odr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> oridevr.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 105 <TR><TD ALIGN=RIGHT> <b><tt>-odt</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> oridevt.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 106 <TR><TD ALIGN=RIGHT> <b><tt>-oten</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  oriten.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 107 <TR><TD ALIGN=RIGHT> <b><tt>-corr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> enecorr.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 108 <TR><TD ALIGN=RIGHT> <b><tt>-vis</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   visco.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 109 <TR><TD ALIGN=RIGHT> <b><tt>-ravg</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">runavgdf.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 110 </TABLE>
 111 <P>
 112 <H3>Other options</H3>
 113 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
 114 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
 115 <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>
 116 <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>
 117 <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>
 118 <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>
 119 <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>
 120 <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>
 121 <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>
 122 <TR><TD ALIGN=RIGHT> <b><tt>-[no]fee</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Do a free energy estimate </TD></TD>
 123 <TR><TD ALIGN=RIGHT> <b><tt>-fetemp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>300   </tt> </TD><TD> Reference temperature for free energy calculation </TD></TD>
 124 <TR><TD ALIGN=RIGHT> <b><tt>-zero</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Subtract a zero-point energy </TD></TD>
 125 <TR><TD ALIGN=RIGHT> <b><tt>-[no]sum</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Sum the energy terms selected rather than display them all </TD></TD>
 126 <TR><TD ALIGN=RIGHT> <b><tt>-[no]dp</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print energies in high precision </TD></TD>
 127 <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 estimate </TD></TD>
 128 <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 estimate </TD></TD>
 129 <TR><TD ALIGN=RIGHT> <b><tt>-[no]mutot</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Compute the total dipole moment from the components </TD></TD>
 130 <TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip number of frames between data points </TD></TD>
 131 <TR><TD ALIGN=RIGHT> <b><tt>-[no]aver</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Also print the exact average and rmsd stored in the energy frames (only when 1 term is requested) </TD></TD>
 132 <TR><TD ALIGN=RIGHT> <b><tt>-nmol</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of molecules in your sample: the energies are divided by this number </TD></TD>
 133 <TR><TD ALIGN=RIGHT> <b><tt>-nconstr</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of constraints per molecule. Necessary for calculating the heat capacity </TD></TD>
 134 <TR><TD ALIGN=RIGHT> <b><tt>-[no]fluc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Calculate autocorrelation of energy fluctuations rather than energy itself </TD></TD>
 135 <TR><TD ALIGN=RIGHT> <b><tt>-[no]orinst</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Analyse instantaneous orientation data </TD></TD>
 136 <TR><TD ALIGN=RIGHT> <b><tt>-[no]ovec</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Also plot the eigenvectors with -oten </TD></TD>
 137 <TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
 138 <TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Normalize ACF </TD></TD>
 139 <TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): <tt>0</tt>, <tt>1</tt>, <tt>2</tt> or <tt>3</tt> </TD></TD>
 140 <TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt> or <tt>exp9</tt> </TD></TD>
 141 <TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
 142 <TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
 143 <TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1    </tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is until the end </TD></TD>
 144 </TABLE>
 145 <P>
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