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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rms</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_rms compares two structures by computing the root mean square
  18 deviation (RMSD), the size-independent 'rho' similarity parameter
  19 (rho) or the scaled rho (rhosc),
  20 see Maiorov & Crippen, PROTEINS <b>22</b>, 273 (1995).
  21 This is selected by <tt>-what</tt>.<p>Each structure from a trajectory (<tt>-f</tt>) is compared to a
  22 reference structure. The reference structure
  23 is taken from the structure file (<tt>-s</tt>).<p>
  24 With option <tt>-mir</tt> also a comparison with the mirror image of
  25 the reference structure is calculated.
  26 This is useful as a reference for 'significant' values, see
  27 Maiorov & Crippen, PROTEINS <b>22</b>, 273 (1995).<p>
  28 Option <tt>-prev</tt> produces the comparison with a previous frame
  29 the specified number of frames ago.<p>
  30 Option <tt>-m</tt> produces a matrix in <tt>.<a href="xpm.html">xpm</a></tt> format of
  31 comparison values of each structure in the trajectory with respect to
  32 each other structure. This file can be visualized with for instance
  33 <tt>xv</tt> and can be converted to postscript with <tt><a href="xpm2ps.html">xpm2ps</a></tt>.<p>
  34 Option <tt>-fit</tt> controls the least-squares fitting of
  35 the structures on <a href="top.html">top</a> of each other: complete fit (rotation and
  36 translation), translation only, or no fitting at all.<p>
  37 Option <tt>-mw</tt> controls whether mass weighting is done or not.
  38 If you select the option (default) and
  39 supply a valid <a href="tpr.html">tpr</a> file masses will be taken from there,
  40 otherwise the masses will be deduced from the atommass.<a href="dat.html">dat</a> file in
  41 the GROMACS library directory. This is fine for proteins but not
  42 necessarily for other molecules. A default mass of 12.011 amu (Carbon)
  43 is assigned to unknown atoms. You can check whether this happend by
  44 turning on the <tt>-debug</tt> flag and inspecting the <a href="log.html">log</a> file.<p>
  45 With <tt>-f2</tt>, the 'other structures' are taken from a second
  46 trajectory, this generates a comparison matrix of one trajectory
  47 versus the other.<p>
  48 Option <tt>-bin</tt> does a binary dump of the comparison matrix.<p>
  49 Option <tt>-bm</tt> produces a matrix of average bond angle deviations
  50 analogously to the <tt>-m</tt> option. Only bonds between atoms in the
  51 comparison group are considered.
  52 <P>
  53 <H3>Files</H3>
  54 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  55 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  56 <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>
  57 <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>
  58 <TR><TD ALIGN=RIGHT> <b><tt>-f2</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>
  59 <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>
  60 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    rmsd.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  61 <TR><TD ALIGN=RIGHT> <b><tt>-mir</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> rmsdmir.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  62 <TR><TD ALIGN=RIGHT> <b><tt>-a</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   avgrp.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  63 <TR><TD ALIGN=RIGHT> <b><tt>-dist</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">rmsd-dist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  64 <TR><TD ALIGN=RIGHT> <b><tt>-m</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">    rmsd.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
  65 <TR><TD ALIGN=RIGHT> <b><tt>-bin</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html">    rmsd.dat</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic data file </TD></TR>
  66 <TR><TD ALIGN=RIGHT> <b><tt>-bm</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">    bond.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
  67 </TABLE>
  68 <P>
  69 <H3>Other options</H3>
  70 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  71 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  72 <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>
  73 <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>
  74 <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>
  75 <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>
  76 <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>
  77 <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>
  78 <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>
  79 <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>
  80 <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>
  81 <TR><TD ALIGN=RIGHT> <b><tt>-what</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>rmsd</tt> </TD><TD> Structural difference measure: <tt>rmsd</tt>, <tt>rho</tt> or <tt>rhosc</tt> </TD></TD>
  82 <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> PBC check </TD></TD>
  83 <TR><TD ALIGN=RIGHT> <b><tt>-fit</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>rot+trans</tt> </TD><TD> Fit to reference structure: <tt>rot+trans</tt>, <tt>translation</tt> or <tt>none</tt> </TD></TD>
  84 <TR><TD ALIGN=RIGHT> <b><tt>-prev</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Compare with previous frame </TD></TD>
  85 <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 graph where time is zero </TD></TD>
  86 <TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Only write every nr-th frame to matrix </TD></TD>
  87 <TR><TD ALIGN=RIGHT> <b><tt>-skip2</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Only write every nr-th frame to matrix </TD></TD>
  88 <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 comparison matrix </TD></TD>
  89 <TR><TD ALIGN=RIGHT> <b><tt>-min</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1    </tt> </TD><TD> Minimum level in comparison matrix </TD></TD>
  90 <TR><TD ALIGN=RIGHT> <b><tt>-bmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1    </tt> </TD><TD> Maximum level in bond angle matrix </TD></TD>
  91 <TR><TD ALIGN=RIGHT> <b><tt>-bmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1    </tt> </TD><TD> Minimum level in bond angle matrix </TD></TD>
  92 <TR><TD ALIGN=RIGHT> <b><tt>-[no]mw</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Use mass weighting for superposition </TD></TD>
  93 <TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>80</tt> </TD><TD> Number of levels in the matrices </TD></TD>
  94 <TR><TD ALIGN=RIGHT> <b><tt>-ng</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of groups to compute RMS between </TD></TD>
  95 </TABLE>
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