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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_angle</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_angle</tt> computes the angle distribution for a number of angles
  18 or dihedrals.<p>
  19 With option <tt>-ov</tt>, you can plot the average angle of
  20 a group of angles as a function of time. With the <tt>-all</tt> option,
  21 the first graph is the average and the rest are the individual angles.<p>
  22 With the <tt>-of</tt> option, <tt>g_angle</tt> also calculates the fraction of trans
  23 dihedrals (only for dihedrals) as function of time, but this is
  24 probably only fun for a select few.<p>
  25 With option <tt>-oc</tt>, a dihedral correlation function is calculated.<p>
  26 It should be noted that the index file must contain
  27 atom triplets for angles or atom quadruplets for dihedrals.
  28 If this is not the case, the program will crash.<p>
  29 With option <tt>-or</tt>, a trajectory file is dumped containing cos and
  30 sin of selected dihedral angles, which subsequently can be used as
  31 input for a principal components analysis using <tt><a href="g_covar.html">g_covar</a></tt>.<p>
  32 Option <tt>-ot</tt> plots when transitions occur between
  33 dihedral rotamers of multiplicity 3 and <tt>-oh</tt>
  34 records a histogram of the times between such transitions,
  35 assuming the input trajectory frames are equally spaced in time.
  36 <P>
  37 <H3>Files</H3>
  38 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  39 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  40 <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>
  41 <TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">   angle.ndx</a></tt> </TD><TD> Input </TD><TD> Index file </TD></TR>
  42 <TR><TD ALIGN=RIGHT> <b><tt>-od</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> angdist.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  43 <TR><TD ALIGN=RIGHT> <b><tt>-ov</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> angaver.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  44 <TR><TD ALIGN=RIGHT> <b><tt>-of</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> dihfrac.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  45 <TR><TD ALIGN=RIGHT> <b><tt>-ot</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">dihtrans.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  46 <TR><TD ALIGN=RIGHT> <b><tt>-oh</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> trhisto.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  47 <TR><TD ALIGN=RIGHT> <b><tt>-oc</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> dihcorr.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  48 <TR><TD ALIGN=RIGHT> <b><tt>-or</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="trr.html">    traj.trr</a></tt> </TD><TD> Output, Opt. </TD><TD> Trajectory in portable xdr format </TD></TR>
  49 </TABLE>
  50 <P>
  51 <H3>Other options</H3>
  52 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  53 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  54 <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>
  55 <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>
  56 <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>
  57 <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>
  58 <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>
  59 <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>
  60 <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>
  61 <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>
  62 <TR><TD ALIGN=RIGHT> <b><tt>-type</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>angle</tt> </TD><TD> Type of angle to analyse: <tt>angle</tt>, <tt>dihedral</tt>, <tt>improper</tt> or <tt>ryckaert-bellemans</tt> </TD></TD>
  63 <TR><TD ALIGN=RIGHT> <b><tt>-[no]all</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Plot all angles separately in the averages file, in the order of appearance in the index file. </TD></TD>
  64 <TR><TD ALIGN=RIGHT> <b><tt>-binwidth</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1     </tt> </TD><TD> binwidth (degrees) for calculating the distribution </TD></TD>
  65 <TR><TD ALIGN=RIGHT> <b><tt>-[no]periodic</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Print dihedral angles modulo 360 degrees </TD></TD>
  66 <TR><TD ALIGN=RIGHT> <b><tt>-[no]chandler</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine correlation function. Trans is defined as phi &lt; -60 or phi &gt; 60. </TD></TD>
  67 <TR><TD ALIGN=RIGHT> <b><tt>-[no]avercorr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Average the correlation functions for the individual angles/dihedrals </TD></TD>
  68 <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>
  69 <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>
  70 <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>
  71 <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>
  72 <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>
  73 <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>
  74 <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>
  75 </TABLE>
  76 <P>
  77 <H3>Known problems</H3>
  78 <UL>
  79 <LI>Counting transitions only works for dihedrals with multiplicity 3
  80 </UL>
  81 <P>
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