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  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>ngmx</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 ngmx is the Gromacs trajectory viewer. This program reads a
  18 trajectory file, a run input file and an index file and plots a
  19 3D structure of your molecule on your standard X Window
  20 screen. No need for a high end graphics workstation, it even
  21 works on Monochrome screens.<p>
  22 The following features have been implemented:
  23 3D view, rotation, translation and scaling of your molecule(s),
  24 labels on atoms, animation of trajectories,
  25 hardcopy in PostScript format, user defined atom-filters
  26 runs on MIT-X (real X), open windows and motif,
  27 user friendly menus, option to remove periodicity, option to
  28 show computational box.<p>
  29 Some of the more common X command line options can be used:<br>
  30 -bg, -fg change colors, -font fontname, changes the font.
  31 <P>
  32 <H3>Files</H3>
  33 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  34 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  35 <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>
  36 <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> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
  37 <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>
  38 </TABLE>
  39 <P>
  40 <H3>Other options</H3>
  41 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  42 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  43 <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>
  44 <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>
  45 <TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
  46 <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>
  47 <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>
  48 <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>
  49 </TABLE>
  50 <P>
  51 <H3>Known problems</H3>
  52 <UL>
  53 <LI>Balls option does not work
  54 <LI>Some times dumps core without a good reason
  55 </UL>
  56 <P>
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  59 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
  60 <font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
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