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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>tpbconv</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 tpbconv can edit run input files in four ways.<p>
  18 <b>1st.</b> by modifying the number of steps in a run input file
  19 with options <tt>-extend</tt>, <tt>-until</tt> or <tt>-nsteps</tt>
  20 (nsteps=-1 means unlimited number of steps)<p>
  21 <b>2nd.</b> (OBSOLETE) by creating a run input file
  22 for a continuation run when your simulation has crashed due to e.g.
  23 a full disk, or by making a continuation run input file.
  24 This option is obsolete, since <a href="mdrun.html">mdrun</a> now writes and reads
  25 checkpoint files.
  26 Note that a frame with coordinates and velocities is needed.
  27 When pressure and/or Nose-Hoover temperature coupling is used
  28 an energy file can be supplied to get an exact continuation
  29 of the original run.<p>
  30 <b>3rd.</b> by creating a tpx file for a subset of your original
  31 tpx file, which is useful when you want to remove the solvent from
  32 your tpx file, or when you want to make e.g. a pure Ca tpx file.
  33 <b>WARNING: this tpx file is not fully functional</b>.
  34 <b>4th.</b> by setting the charges of a specified group
  35 to zero. This is useful when doing free energy estimates
  36 using the LIE (Linear Interaction Energy) method.
  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>-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>
  42 <TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    traj.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>
  43 <TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edr.html">    ener.edr</a></tt> </TD><TD> Input, Opt. </TD><TD> Energy file </TD></TR>
  44 <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>
  45 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">  tpxout.tpr</a></tt> </TD><TD> Output </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>
  46 </TABLE>
  47 <P>
  48 <H3>Other options</H3>
  49 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  50 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  51 <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>
  52 <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>
  53 <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>
  54 <TR><TD ALIGN=RIGHT> <b><tt>-extend</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Extend runtime by this amount (ps) </TD></TD>
  55 <TR><TD ALIGN=RIGHT> <b><tt>-until</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Extend runtime until this ending time (ps) </TD></TD>
  56 <TR><TD ALIGN=RIGHT> <b><tt>-nsteps</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Change the number of steps </TD></TD>
  57 <TR><TD ALIGN=RIGHT> <b><tt>-time</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1    </tt> </TD><TD> Continue from frame at this time (ps) instead of the last frame </TD></TD>
  58 <TR><TD ALIGN=RIGHT> <b><tt>-[no]zeroq</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Set the charges of a group (from the index) to zero </TD></TD>
  59 <TR><TD ALIGN=RIGHT> <b><tt>-[no]vel</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Require velocities from trajectory </TD></TD>
  60 <TR><TD ALIGN=RIGHT> <b><tt>-[no]cont</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> For exact continuation, the constraints should not be applied before the first step </TD></TD>
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