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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_current</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 This is a tool for calculating the current autocorrelation function, the correlation
  18 of the rotational and translational dipole moment of the system, and the resulting static
  19 dielectric constant. To obtain a reasonable result the index group has to be neutral.
  20 Furthermore the routine is capable of extracting the static conductivity from the current
  21 autocorrelation function, if velocities are given. Additionally an Einstein-Helfand fit also
  22 allows to get the static conductivity.<p>
  23 The flag <tt>-caf</tt> is for the output of the current autocorrelation function and <tt>-mc</tt> writes the
  24 correlation of the rotational and translational part of the dipole moment in the corresponding
  25 file. However this option is only available for trajectories containing velocities.
  26 Options <tt>-sh</tt> and <tt>-tr</tt> are responsible for the averaging and integration of the
  27 autocorrelation functions. Since averaging proceeds by shifting the starting point
  28 through the trajectory, the shift can be modified with <tt>-sh</tt> to enable the choice of uncorrelated
  29 starting points. Towards the end, statistical inaccuracy grows and integrating the
  30 correlation function only yields reliable values until a certain point, depending on
  31 the number of frames. The option <tt>-tr</tt> controls the region of the integral taken into account
  32 for calculating the static dielectric constant.
  33 <p>
  34 Option <tt>-temp</tt> sets the temperature required for the computation of the static dielectric constant.
  35 <p>
  36 Option <tt>-<a href="eps.html">eps</a></tt> controls the dielectric constant of the surrounding medium for simulations using
  37 a Reaction Field or dipole corrections of the Ewald summation (<a href="eps.html">eps</a>=0 corresponds to
  38 tin-foil boundary conditions).
  39 <p>
  40 <tt>-[no]nojump</tt> unfolds the coordinates to allow free diffusion. This is required to get a continuous
  41 translational dipole moment, required for the Einstein-Helfand fit. The resuls from the fit allow to
  42 determine the dielectric constant for system of charged molecules. However it is also possible to extract
  43 the dielectric constant from the fluctuations of the total dipole moment in folded coordinates. But this
  44 options has to be used with care, since only very short time spans fulfill the approximation, that the density
  45 of the molecules is approximately constant and the averages are already converged. To be on the safe side,
  46 the dielectric constant should be calculated with the help of the Einstein-Helfand method for
  47 the translational part of the dielectric constant.
  48 <P>
  49 <H3>Files</H3>
  50 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  51 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  52 <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 </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
  53 <TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">   index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
  54 <TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
  55 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> current.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  56 <TR><TD ALIGN=RIGHT> <b><tt>-caf</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">     caf.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  57 <TR><TD ALIGN=RIGHT> <b><tt>-dsp</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">     dsp.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  58 <TR><TD ALIGN=RIGHT> <b><tt>-md</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">      md.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  59 <TR><TD ALIGN=RIGHT> <b><tt>-mj</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">      mj.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  60 <TR><TD ALIGN=RIGHT> <b><tt>-mc</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">      mc.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  61 </TABLE>
  62 <P>
  63 <H3>Other options</H3>
  64 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  65 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  66 <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>
  67 <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>
  68 <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>
  69 <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>
  70 <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>
  71 <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>
  72 <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>
  73 <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>
  74 <TR><TD ALIGN=RIGHT> <b><tt>-sh</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1000</tt> </TD><TD> Shift of the frames for averaging the correlation functions and the mean-square displacement. </TD></TD>
  75 <TR><TD ALIGN=RIGHT> <b><tt>-[no]nojump</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Removes jumps of atoms across the box. </TD></TD>
  76 <TR><TD ALIGN=RIGHT> <b><tt>-eps</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Dielectric constant of the surrounding medium. <a href="eps.html">eps</a>=0.0 corresponds to <a href="eps.html">eps</a>=infinity (thinfoil boundary conditions). </TD></TD>
  77 <TR><TD ALIGN=RIGHT> <b><tt>-bfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>100   </tt> </TD><TD> Begin of the fit of the straight line to the MSD of the translational fraction of the dipole moment. </TD></TD>
  78 <TR><TD ALIGN=RIGHT> <b><tt>-efit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>400   </tt> </TD><TD> End of the fit of the straight line to the MSD of the translational fraction of the dipole moment. </TD></TD>
  79 <TR><TD ALIGN=RIGHT> <b><tt>-bvit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.5   </tt> </TD><TD> Begin of the fit of the current autocorrelation function to a*t^b. </TD></TD>
  80 <TR><TD ALIGN=RIGHT> <b><tt>-evit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>5     </tt> </TD><TD> End of the fit of the current autocorrelation function to a*t^b. </TD></TD>
  81 <TR><TD ALIGN=RIGHT> <b><tt>-tr</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.25  </tt> </TD><TD> Fraction of the trajectory taken into account for the integral. </TD></TD>
  82 <TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>300   </tt> </TD><TD> Temperature for calculating epsilon. </TD></TD>
  83 </TABLE>
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