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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_tcaf</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_tcaf computes tranverse current autocorrelations.
  18 These are used to estimate the shear viscosity eta.
  19 For details see: Palmer, JCP 49 (1994) pp 359-366.<p>
  20 Transverse currents are calculated using the
  21 k-vectors (1,0,0) and (2,0,0) each also in the y- and z-direction,
  22 (1,1,0) and (1,-1,0) each also in the 2 other planes (these vectors
  23 are not independent) and (1,1,1) and the 3 other box diagonals (also
  24 not independent). For each k-vector the sine and cosine are used, in
  25 combination with the velocity in 2 perpendicular directions. This gives
  26 a total of 16*2*2=64 transverse currents. One autocorrelation is
  27 calculated fitted for each k-vector, which gives 16 tcaf's. Each of
  28 these tcaf's is fitted to f(t) = exp(-v)(cosh(Wv) + 1/W sinh(Wv)),
  29 v = -t/(2 tau), W = sqrt(1 - 4 tau eta/rho k^2), which gives 16 tau's
  30 and eta's. The fit weights decay with time as exp(-t/wt), the tcaf and
  31 fit are calculated up to time 5*wt.
  32 The eta's should be fitted to 1 - a eta(k) k^2, from which
  33 one can estimate the shear viscosity at k=0.<p>
  34 When the box is cubic, one can use the option <tt>-oc</tt>, which
  35 averages the tcaf's over all k-vectors with the same length.
  36 This results in more accurate tcaf's.
  37 Both the cubic tcaf's and fits are written to <tt>-oc</tt>
  38 The cubic eta estimates are also written to <tt>-ov</tt>.<p>
  39 With option <tt>-mol</tt> the transverse current is determined of
  40 molecules instead of atoms. In this case the index group should
  41 consist of molecule numbers instead of atom numbers.<p>
  42 The k-dependent viscosities in the <tt>-ov</tt> file should be
  43 fitted to eta(k) = eta0 (1 - a k^2) to obtain the viscosity at
  44 infinite wavelength.<p>
  45 NOTE: make sure you write coordinates and velocities often enough.
  46 The initial, non-exponential, part of the autocorrelation function
  47 is very important for obtaining a good fit.
  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>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    traj.trr</a></tt> </TD><TD> Input </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
  53 <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> 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>
  54 <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>
  55 <TR><TD ALIGN=RIGHT> <b><tt>-ot</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">transcur.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  56 <TR><TD ALIGN=RIGHT> <b><tt>-oa</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">tcaf_all.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  57 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    tcaf.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  58 <TR><TD ALIGN=RIGHT> <b><tt>-of</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">tcaf_fit.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  59 <TR><TD ALIGN=RIGHT> <b><tt>-oc</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">tcaf_cub.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  60 <TR><TD ALIGN=RIGHT> <b><tt>-ov</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  visc_k.xvg</a></tt> </TD><TD> Output </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>19</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>-[no]mol</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Calculate tcaf of molecules </TD></TD>
  75 <TR><TD ALIGN=RIGHT> <b><tt>-[no]k34</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Also use k=(3,0,0) and k=(4,0,0) </TD></TD>
  76 <TR><TD ALIGN=RIGHT> <b><tt>-wt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>5     </tt> </TD><TD> Exponential decay time for the TCAF fit weights </TD></TD>
  77 <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>
  78 <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>
  79 <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>
  80 <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>
  81 <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>
  82 <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>
  83 <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>
  84 </TABLE>
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