share/html/online/g_rmsdist.html

   1 <HTML>
   2 <HEAD>
   3 <TITLE>g_rmsdist</TITLE>
   4 <LINK rel=stylesheet href="style.css" type="text/css">
   5 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
   6 <TABLE WIDTH="98%" NOBORDER >
   7 <TR><TD WIDTH=400>
   8 <TABLE WIDTH=400 NOBORDER>
   9 <TD WIDTH=116>
  10 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rmsdist</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-beta4-2010-08-26 09:43:57 +0200-33da7ba-dirty<br>
  13 Thu 26 Aug 2010</B></td></tr></TABLE>
  14 <HR>
  15 <H3>Description</H3>
  16 <p>
  17 g_rmsdist computes the root mean square deviation of atom distances,
  18 which has the advantage that no fit is needed like in standard RMS
  19 deviation as computed by <a href="g_rms.html">g_rms</a>.
  20 The reference structure is taken from the structure file.
  21 The rmsd at time t is calculated as the rms
  22 of the differences in distance between atom-pairs in the reference
  23 structure and the structure at time t.<p>
  24 g_rmsdist can also produce matrices of the rms distances, rms distances
  25 scaled with the mean distance and the mean distances and matrices with
  26 NMR averaged distances (1/r^3 and 1/r^6 averaging). Finally, lists
  27 of atom pairs with 1/r^3 and 1/r^6 averaged distance below the
  28 maximum distance (<tt>-max</tt>, which will default to 0.6 in this case)
  29 can be generated, by default averaging over equivalent hydrogens
  30 (all triplets of hydrogens named *[123]). Additionally a list of
  31 equivalent atoms can be supplied (<tt>-equiv</tt>), each line containing
  32 a set of equivalent atoms specified as residue number and name and
  33 atom name; e.g.:<p>
  34 <tt>3 SER  HB1 3 SER  HB2</tt><p>
  35 Residue and atom names must exactly match those in the structure
  36 file, including case. Specifying non-sequential atoms is undefined.
  37 <P>
  38 <H3>Files</H3>
  39 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  40 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  41 <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>
  42 <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>
  43 <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>
  44 <TR><TD ALIGN=RIGHT> <b><tt>-equiv</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html">   equiv.dat</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic data file </TD></TR>
  45 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">distrmsd.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  46 <TR><TD ALIGN=RIGHT> <b><tt>-rms</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> rmsdist.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
  47 <TR><TD ALIGN=RIGHT> <b><tt>-scl</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">rmsscale.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
  48 <TR><TD ALIGN=RIGHT> <b><tt>-mean</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> rmsmean.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
  49 <TR><TD ALIGN=RIGHT> <b><tt>-nmr3</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">    nmr3.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
  50 <TR><TD ALIGN=RIGHT> <b><tt>-nmr6</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">    nmr6.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
  51 <TR><TD ALIGN=RIGHT> <b><tt>-noe</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html">     noe.dat</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic data file </TD></TR>
  52 </TABLE>
  53 <P>
  54 <H3>Other options</H3>
  55 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  56 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  57 <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>
  58 <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>
  59 <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>
  60 <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>
  61 <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>
  62 <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>
  63 <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>
  64 <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>
  65 <TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>40</tt> </TD><TD> Discretize rms in # levels </TD></TD>
  66 <TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1    </tt> </TD><TD> Maximum level in matrices </TD></TD>
  67 <TR><TD ALIGN=RIGHT> <b><tt>-[no]sumh</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> average distance over equivalent hydrogens </TD></TD>
  68 <TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Use periodic boundary conditions when computing distances </TD></TD>
  69 </TABLE>
  70 <P>
  71 <hr>
  72 <div ALIGN=RIGHT>
  73 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
  74 <font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
  75 </div>
  76 </BODY>