share/html/online/g_traj.html

   1 <HTML>
   2 <HEAD>
   3 <TITLE>g_traj</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_traj</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>
  14 <HR>
  15 <H3>Description</H3>
  16 <p>
  17 g_traj plots coordinates, velocities, forces and/or the box.
  18 With <tt>-com</tt> the coordinates, velocities and forces are
  19 calculated for the center of mass of each group.
  20 When <tt>-mol</tt> is set, the numbers in the index file are
  21 interpreted as molecule numbers and the same procedure as with
  22 <tt>-com</tt> is used for each molecule.<p>
  23 Option <tt>-ot</tt> plots the temperature of each group,
  24 provided velocities are present in the trajectory file.
  25 No corrections are made for constrained degrees of freedom!
  26 This implies <tt>-com</tt>.<p>
  27 Options <tt>-ekt</tt> and <tt>-ekr</tt> plot the translational and
  28 rotational kinetic energy of each group,
  29 provided velocities are present in the trajectory file.
  30 This implies <tt>-com</tt>.<p>
  31 Options <tt>-cv</tt> and <tt>-cf</tt> write the average velocities
  32 and average forces as temperature factors to a <a href="pdb.html">pdb</a> file with
  33 the average coordinates. The temperature factors are scaled such
  34 that the maximum is 10. The scaling can be changed with the option
  35 <tt>-scale</tt>. To get the velocities or forces of one
  36 frame set both <tt>-b</tt> and <tt>-e</tt> to the time of
  37 desired frame. When averaging over frames you might need to use
  38 the <tt>-nojump</tt> option to obtain the correct average coordinates.
  39 If you select either of these option the average force and velocity
  40 for each atom are written to an <a href="xvg.html">xvg</a> file as well
  41 (specified with <tt>-av</tt> or <tt>-af</tt>).<p>
  42 Option <tt>-vd</tt> computes a velocity distribution, i.e. the
  43 norm of the vector is plotted. In addition in the same graph
  44 the kinetic energy distribution is given.
  45 <P>
  46 <H3>Files</H3>
  47 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  48 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  49 <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>
  50 <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>
  51 <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>
  52 <TR><TD ALIGN=RIGHT> <b><tt>-ox</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   coord.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  53 <TR><TD ALIGN=RIGHT> <b><tt>-oxt</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   coord.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>
  54 <TR><TD ALIGN=RIGHT> <b><tt>-ov</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   veloc.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  55 <TR><TD ALIGN=RIGHT> <b><tt>-of</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   force.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  56 <TR><TD ALIGN=RIGHT> <b><tt>-ob</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">     box.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  57 <TR><TD ALIGN=RIGHT> <b><tt>-ot</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    temp.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  58 <TR><TD ALIGN=RIGHT> <b><tt>-ekt</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> ektrans.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  59 <TR><TD ALIGN=RIGHT> <b><tt>-ekr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   ekrot.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  60 <TR><TD ALIGN=RIGHT> <b><tt>-vd</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> veldist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  61 <TR><TD ALIGN=RIGHT> <b><tt>-cv</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html">   veloc.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Protein data bank file </TD></TR>
  62 <TR><TD ALIGN=RIGHT> <b><tt>-cf</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html">   force.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Protein data bank file </TD></TR>
  63 <TR><TD ALIGN=RIGHT> <b><tt>-av</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">all_veloc.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  64 <TR><TD ALIGN=RIGHT> <b><tt>-af</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">all_force.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  65 </TABLE>
  66 <P>
  67 <H3>Other options</H3>
  68 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  69 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  70 <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>
  71 <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>
  72 <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>
  73 <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>
  74 <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>
  75 <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>
  76 <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>
  77 <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>
  78 <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>
  79 <TR><TD ALIGN=RIGHT> <b><tt>-[no]com</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Plot data for the com of each group </TD></TD>
  80 <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> Make molecules whole for COM </TD></TD>
  81 <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> Index contains molecule numbers iso atom numbers </TD></TD>
  82 <TR><TD ALIGN=RIGHT> <b><tt>-[no]nojump</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Remove jumps of atoms across the box </TD></TD>
  83 <TR><TD ALIGN=RIGHT> <b><tt>-[no]x</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Plot X-component </TD></TD>
  84 <TR><TD ALIGN=RIGHT> <b><tt>-[no]y</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Plot Y-component </TD></TD>
  85 <TR><TD ALIGN=RIGHT> <b><tt>-[no]z</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Plot Z-component </TD></TD>
  86 <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 consider </TD></TD>
  87 <TR><TD ALIGN=RIGHT> <b><tt>-[no]len</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Plot vector length </TD></TD>
  88 <TR><TD ALIGN=RIGHT> <b><tt>-[no]fp</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Full precision output </TD></TD>
  89 <TR><TD ALIGN=RIGHT> <b><tt>-bin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1     </tt> </TD><TD> Binwidth for velocity histogram (nm/ps) </TD></TD>
  90 <TR><TD ALIGN=RIGHT> <b><tt>-scale</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Scale factor for <a href="pdb.html">pdb</a> output, 0 is autoscale </TD></TD>
  91 </TABLE>
  92 <P>
  93 <hr>
  94 <div ALIGN=RIGHT>
  95 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
  96 <font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
  97 </div>
  98 </BODY>