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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_mindist</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_mindist computes the distance between one group and a number of
  18 other groups. Both the minimum distance
  19 (between any pair of atoms from the respective groups)
  20 and the number of contacts within a given
  21 distance are written to two separate output files.
  22 With the <tt>-group</tt> option a contact of an atom an other group
  23 with multiple atoms in the first group is counted as one contact
  24 instead of as multiple contacts.
  25 With <tt>-or</tt>, minimum distances to each residue in the first
  26 group are determined and plotted as a function of residue number.<p>
  27 With option <tt>-pi</tt> the minimum distance of a group to its
  28 periodic image is plotted. This is useful for checking if a protein
  29 has seen its periodic image during a simulation. Only one shift in
  30 each direction is considered, giving a total of 26 shifts.
  31 It also plots the maximum distance within the group and the lengths
  32 of the three box vectors.<p>
  33 Other programs that calculate distances are <tt><a href="g_dist.html">g_dist</a></tt>
  34 and <tt><a href="g_bond.html">g_bond</a></tt>.
  35 <P>
  36 <H3>Files</H3>
  37 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  38 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  39 <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>
  40 <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, Opt. </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>
  41 <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>
  42 <TR><TD ALIGN=RIGHT> <b><tt>-od</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> mindist.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  43 <TR><TD ALIGN=RIGHT> <b><tt>-on</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> numcont.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  44 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="out.html">atm-pair.out</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic output file </TD></TR>
  45 <TR><TD ALIGN=RIGHT> <b><tt>-ox</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> mindist.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> </TD></TR>
  46 <TR><TD ALIGN=RIGHT> <b><tt>-or</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">mindistres.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
  47 </TABLE>
  48 <P>
  49 <H3>Other options</H3>
  50 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  51 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  52 <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>
  53 <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>
  54 <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>
  55 <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>
  56 <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>
  57 <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>
  58 <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>
  59 <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>
  60 <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>
  61 <TR><TD ALIGN=RIGHT> <b><tt>-[no]matrix</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Calculate half a matrix of group-group distances </TD></TD>
  62 <TR><TD ALIGN=RIGHT> <b><tt>-[no]max</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Calculate *maximum* distance instead of minimum </TD></TD>
  63 <TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.6   </tt> </TD><TD> Distance for contacts </TD></TD>
  64 <TR><TD ALIGN=RIGHT> <b><tt>-[no]group</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Count contacts with multiple atoms in the first group as one </TD></TD>
  65 <TR><TD ALIGN=RIGHT> <b><tt>-[no]pi</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Calculate minimum distance with periodic images </TD></TD>
  66 <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>
  67 <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 secondary groups to compute distance to a central group </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> Take periodic boundary conditions into account </TD></TD>
  69 <TR><TD ALIGN=RIGHT> <b><tt>-[no]respertime</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> When writing per-residue distances, write distance for each time point </TD></TD>
  70 <TR><TD ALIGN=RIGHT> <b><tt>-[no]printresname</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Write residue names </TD></TD>
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