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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 4.6<br>
  13 Sat 19 Jan 2013</B></td></tr></TABLE>
  14 <HR>
  15 <H3>Description</H3>
  16 <p>
  17 <tt>g_energy</tt> extracts energy components or distance restraint
  18 data from an energy file. The user is prompted to interactively
  19 select the desired energy terms.<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 least-squares 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 <b>Note</b> 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 <tt>g_energy</tt> statistics output more accurate
  31 than the <tt>.<a href="xvg.html">xvg</a></tt> output. When exact averages are not present in the energy
  32 file, the statistics mentioned above are simply over the single, per-frame
  33 energy values.<p>
  34 The term fluctuation gives the RMSD around the least-squares fit.<p>
  35 Some fluctuation-dependent properties can be calculated provided
  36 the correct energy terms are selected, and that the command line option
  37 <tt>-fluct_props</tt> is given. The following properties
  38 will be computed:<br>
  39 Property                        Energy terms needed<br>
  40 ---------------------------------------------------<br>
  41 Heat capacity C_p (NPT sims):    Enthalpy, Temp     <br>
  42 Heat capacity C_v (NVT sims):    Etot, Temp         <br>
  43 Thermal expansion coeff. (NPT): Enthalpy, Vol, Temp<br>
  44 Isothermal compressibility:     Vol, Temp          <br>
  45 Adiabatic bulk modulus:         Vol, Temp          <br>
  46 ---------------------------------------------------<br>
  47 You always need to set the number of molecules <tt>-nmol</tt>.
  48 The C_p/C_v computations do <b>not</b> include any corrections
  49 for quantum effects. Use the <tt>g_dos</tt> program if you need that (and you do).<p>When the <tt>-viol</tt> option is set, the time averaged
  50 violations are plotted and the running time-averaged and
  51 instantaneous sum of violations are recalculated. Additionally
  52 running time-averaged and instantaneous distances between
  53 selected pairs can be plotted with the <tt>-pairs</tt> option.<p>
  54 Options <tt>-ora</tt>, <tt>-ort</tt>, <tt>-oda</tt>, <tt>-odr</tt> and
  55 <tt>-odt</tt> are used for analyzing orientation restraint data.
  56 The first two options plot the orientation, the last three the
  57 deviations of the orientations from the experimental values.
  58 The options that end on an 'a' plot the average over time
  59 as a function of restraint. The options that end on a 't'
  60 prompt the user for restraint label numbers and plot the data
  61 as a function of time. Option <tt>-odr</tt> plots the RMS
  62 deviation as a function of restraint.
  63 When the run used time or ensemble averaged orientation restraints,
  64 option <tt>-orinst</tt> can be used to analyse the instantaneous,
  65 not ensemble-averaged orientations and deviations instead of
  66 the time and ensemble averages.<p>
  67 Option <tt>-oten</tt> plots the eigenvalues of the molecular order
  68 tensor for each orientation restraint experiment. With option
  69 <tt>-ovec</tt> also the eigenvectors are plotted.<p>
  70 Option <tt>-odh</tt> extracts and plots the free energy data
  71 (Hamiltoian differences and/or the Hamiltonian derivative dhdl)
  72 from the <tt>ener.<a href="edr.html">edr</a></tt> file.<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_idealgas(N,V,T) = kT ln(<exp(U_pot/kT)>)<br>
  76   &Delta; G = G(N,p,T) - G_idealgas(N,p,T) = kT ln(<exp(U_pot/kT)>)<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_idealgas(N,V,T) = (<U_pot> - &Delta; A)/T<br>
  84   &Delta; S(N,p,T) = S(N,p,T) - S_idealgas(N,p,T) = (<U_pot> + pV - &Delta; G)/T
  85 <p>
  86 When a second energy file is specified (<tt>-f2</tt>), a free energy
  87 difference is calculated <br> dF = -kT ln(<exp(-(E_B-E_A)/kT)>_A) ,
  88 where E_A and E_B are the energies from the first and second energy
  89 files, and the average is over the ensemble A. The running average
  90 of the free energy difference is printed to a file specified by <tt>-ravg</tt>.
  91 <b>Note</b> that the energies must both be calculated from the same trajectory.
  92 <P>
  93 <H3>Files</H3>
  94 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  95 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  96 <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>
  97 <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>
  98 <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>
  99 <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>
 100 <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>
 101 <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>
 102 <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>
 103 <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>
 104 <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>
 105 <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>
 106 <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>
 107 <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>
 108 <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>
 109 <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>
 110 <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>
 111 <TR><TD ALIGN=RIGHT> <b><tt>-odh</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    dhdl.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 112 </TABLE>
 113 <P>
 114 <H3>Other options</H3>
 115 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
 116 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
 117 <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>
 118 <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>
 119 <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>
 120 <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>
 121 <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>
 122 <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>
 123 <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>
 124 <TR><TD ALIGN=RIGHT> <b><tt>-[no]fee</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Do a free energy estimate </TD></TD>
 125 <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>
 126 <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>
 127 <TR><TD ALIGN=RIGHT> <b><tt>-[no]sum</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Sum the energy terms selected rather than display them all </TD></TD>
 128 <TR><TD ALIGN=RIGHT> <b><tt>-[no]dp</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print energies in high precision </TD></TD>
 129 <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>
 130 <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>
 131 <TR><TD ALIGN=RIGHT> <b><tt>-[no]mutot</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Compute the total dipole moment from the components </TD></TD>
 132 <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>
 133 <TR><TD ALIGN=RIGHT> <b><tt>-[no]aver</tt></b> </TD><TD ALIGN=RIGHT> 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>
 134 <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>
 135 <TR><TD ALIGN=RIGHT> <b><tt>-[no]fluct_props</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Compute properties based on energy fluctuations, like heat capacity </TD></TD>
 136 <TR><TD ALIGN=RIGHT> <b><tt>-[no]driftcorr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Useful only for calculations of fluctuation properties. The drift in the observables will be subtracted before computing the fluctuation properties. </TD></TD>
 137 <TR><TD ALIGN=RIGHT> <b><tt>-[no]fluc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Calculate autocorrelation of energy fluctuations rather than energy itself </TD></TD>
 138 <TR><TD ALIGN=RIGHT> <b><tt>-[no]orinst</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Analyse instantaneous orientation data </TD></TD>
 139 <TR><TD ALIGN=RIGHT> <b><tt>-[no]ovec</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Also plot the eigenvectors with <tt>-oten</tt> </TD></TD>
 140 <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>
 141 <TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Normalize ACF </TD></TD>
 142 <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>
 143 <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>, <tt>exp9</tt> or <tt>erffit</tt> </TD></TD>
 144 <TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip this many points in the output file of correlation functions </TD></TD>
 145 <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>
 146 <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>
 147 </TABLE>
 148 <P>
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