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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_anaeig</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 <tt>g_anaeig</tt> analyzes eigenvectors. The eigenvectors can be of a
  18 covariance matrix (<tt><a href="g_covar.html">g_covar</a></tt>) or of a Normal Modes analysis
  19 (<tt><a href="g_nmeig.html">g_nmeig</a></tt>).<p>
  20 When a trajectory is projected on eigenvectors, all structures are
  21 fitted to the structure in the eigenvector file, if present, otherwise
  22 to the structure in the structure file. When no run input file is
  23 supplied, periodicity will not be taken into account. Most analyses
  24 are performed on eigenvectors <tt>-first</tt> to <tt>-last</tt>, but when
  25 <tt>-first</tt> is set to -1 you will be prompted for a selection.<p>
  26 <tt>-comp</tt>: plot the vector components per atom of eigenvectors
  27 <tt>-first</tt> to <tt>-last</tt>.<p>
  28 <tt>-rmsf</tt>: plot the RMS fluctuation per atom of eigenvectors
  29 <tt>-first</tt> to <tt>-last</tt> (requires <tt>-eig</tt>).<p>
  30 <tt>-proj</tt>: calculate projections of a trajectory on eigenvectors
  31 <tt>-first</tt> to <tt>-last</tt>.
  32 The projections of a trajectory on the eigenvectors of its
  33 covariance matrix are called principal components (pc's).
  34 It is often useful to check the cosine content of the pc's,
  35 since the pc's of random diffusion are cosines with the number
  36 of periods equal to half the pc index.
  37 The cosine content of the pc's can be calculated with the program
  38 <tt><a href="g_analyze.html">g_analyze</a></tt>.<p>
  39 <tt>-2d</tt>: calculate a 2d projection of a trajectory on eigenvectors
  40 <tt>-first</tt> and <tt>-last</tt>.<p>
  41 <tt>-3d</tt>: calculate a 3d projection of a trajectory on the first
  42 three selected eigenvectors.<p>
  43 <tt>-filt</tt>: filter the trajectory to show only the motion along
  44 eigenvectors <tt>-first</tt> to <tt>-last</tt>.<p>
  45 <tt>-extr</tt>: calculate the two extreme projections along a trajectory
  46 on the average structure and interpolate <tt>-nframes</tt> frames
  47 between them, or set your own extremes with <tt>-max</tt>. The
  48 eigenvector <tt>-first</tt> will be written unless <tt>-first</tt> and
  49 <tt>-last</tt> have been set explicitly, in which case all eigenvectors
  50 will be written to separate files. Chain identifiers will be added
  51 when writing a <tt>.<a href="pdb.html">pdb</a></tt> file with two or three structures (you
  52 can use <tt>rasmol -nmrpdb</tt> to view such a <a href="pdb.html">pdb</a> file).<p>
  53   Overlap calculations between covariance analysis:<br>
  54   NOTE: the analysis should use the same fitting structure<p>
  55 <tt>-over</tt>: calculate the subspace overlap of the eigenvectors in
  56 file <tt>-v2</tt> with eigenvectors <tt>-first</tt> to <tt>-last</tt>
  57 in file <tt>-v</tt>.<p>
  58 <tt>-inpr</tt>: calculate a matrix of inner-products between
  59 eigenvectors in files <tt>-v</tt> and <tt>-v2</tt>. All eigenvectors
  60 of both files will be used unless <tt>-first</tt> and <tt>-last</tt>
  61 have been set explicitly.<p>
  62 When <tt>-v</tt>, <tt>-eig</tt>, <tt>-v2</tt> and <tt>-eig2</tt> are given,
  63 a single number for the overlap between the covariance matrices is
  64 generated. The formulas are:<br>
  65         difference = sqrt(tr((sqrt(M1) - sqrt(M2))^2))<br>
  66 normalized overlap = 1 - difference/sqrt(tr(M1) + tr(M2))<br>
  67      shape overlap = 1 - sqrt(tr((sqrt(M1/tr(M1)) - sqrt(M2/tr(M2)))^2))<br>
  68 where M1 and M2 are the two covariance matrices and tr is the trace
  69 of a matrix. The numbers are proportional to the overlap of the square
  70 root of the fluctuations. The normalized overlap is the most useful
  71 number, it is 1 for identical matrices and 0 when the sampled
  72 subspaces are orthogonal.<p>
  73 When the <tt>-entropy</tt> flag is given an entropy estimate will be
  74 computed based on the Quasiharmonic approach and based on
  75 Schlitter's formula.
  76 <P>
  77 <H3>Files</H3>
  78 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  79 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  80 <TR><TD ALIGN=RIGHT> <b><tt>-v</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">eigenvec.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>
  81 <TR><TD ALIGN=RIGHT> <b><tt>-v2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">eigenvec2.trr</a></tt> </TD><TD> Input, Opt. </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
  82 <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, Opt. </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>
  83 <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>
  84 <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>
  85 <TR><TD ALIGN=RIGHT> <b><tt>-eig</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">eigenval.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  86 <TR><TD ALIGN=RIGHT> <b><tt>-eig2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">eigenval2.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  87 <TR><TD ALIGN=RIGHT> <b><tt>-comp</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> eigcomp.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  88 <TR><TD ALIGN=RIGHT> <b><tt>-rmsf</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> eigrmsf.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  89 <TR><TD ALIGN=RIGHT> <b><tt>-proj</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    proj.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  90 <TR><TD ALIGN=RIGHT> <b><tt>-2d</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  2dproj.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  91 <TR><TD ALIGN=RIGHT> <b><tt>-3d</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">  3dproj.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> etc. </TD></TR>
  92 <TR><TD ALIGN=RIGHT> <b><tt>-filt</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">filtered.xtc</a></tt> </TD><TD> Output, Opt. </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>
  93 <TR><TD ALIGN=RIGHT> <b><tt>-extr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> extreme.pdb</a></tt> </TD><TD> Output, Opt. </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>
  94 <TR><TD ALIGN=RIGHT> <b><tt>-over</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> overlap.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  95 <TR><TD ALIGN=RIGHT> <b><tt>-inpr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">  inprod.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
  96 </TABLE>
  97 <P>
  98 <H3>Other options</H3>
  99 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
 100 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
 101 <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>
 102 <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>
 103 <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>
 104 <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>
 105 <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>
 106 <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>
 107 <TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>fs</tt>, <tt>ps</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
 108 <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>
 109 <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>
 110 <TR><TD ALIGN=RIGHT> <b><tt>-first</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> First eigenvector for analysis (-1 is select) </TD></TD>
 111 <TR><TD ALIGN=RIGHT> <b><tt>-last</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>8</tt> </TD><TD> Last eigenvector for analysis (-1 is till the last) </TD></TD>
 112 <TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Only analyse every nr-th frame </TD></TD>
 113 <TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Maximum for projection of the eigenvector on the average structure, max=0 gives the extremes </TD></TD>
 114 <TR><TD ALIGN=RIGHT> <b><tt>-nframes</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>2</tt> </TD><TD> Number of frames for the extremes output </TD></TD>
 115 <TR><TD ALIGN=RIGHT> <b><tt>-[no]split</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Split eigenvector projections where time is zero </TD></TD>
 116 <TR><TD ALIGN=RIGHT> <b><tt>-[no]entropy</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Compute entropy according to the Quasiharmonic formula or Schlitter's method. </TD></TD>
 117 <TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>298.15</tt> </TD><TD> Temperature for entropy calculations </TD></TD>
 118 <TR><TD ALIGN=RIGHT> <b><tt>-nevskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>6</tt> </TD><TD> Number of eigenvalues to skip when computing the entropy due to the quasi harmonic approximation. When you do a rotational and/or translational fit prior to the covariance analysis, you get 3 or 6 eigenvalues that are very close to zero, and which should not be taken into account when computing the entropy. </TD></TD>
 119 </TABLE>
 120 <P>
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