share/html/online/genrestr.html

   1 <HTML>
   2 <HEAD>
   3 <TITLE>genrestr</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>genrestr</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 4.6<br>
  13 Sat 19 Jan 2013</B></td></tr></TABLE>
  14 <HR>
  15 <H3>Description</H3>
  16 <p>
  17 <tt>genrestr</tt> produces an include file for a topology containing
  18 a list of atom numbers and three force constants for the
  19 <it>x</it>-, <it>y</it>-, and <it>z</it>-direction. A single isotropic force constant may
  20 be given on the command line instead of three components.<p>
  21 WARNING: position restraints only work for the one molecule at a time.
  22 Position restraints are interactions within molecules, therefore
  23 they should be included within the correct <tt>[ moleculetype ]</tt>
  24 block in the topology. Since the atom numbers in every moleculetype
  25 in the topology start at 1 and the numbers in the input file for
  26 <tt>genrestr</tt> number consecutively from 1, <tt>genrestr</tt> will only
  27 produce a useful file for the first molecule.<p>
  28 The <tt>-of</tt> option produces an index file that can be used for
  29 freezing atoms. In this case, the input file must be a <tt>.<a href="pdb.html">pdb</a></tt> file.<p>
  30 With the <tt>-disre</tt> option, half a matrix of distance restraints
  31 is generated instead of position restraints. With this matrix, that
  32 one typically would apply to C&alpha; atoms in a protein, one can
  33 maintain the overall conformation of a protein without tieing it to
  34 a specific position (as with position restraints).
  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">    conf.gro</a></tt> </TD><TD> Input </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> etc. </TD></TR>
  40 <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>
  41 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="itp.html">   posre.itp</a></tt> </TD><TD> Output </TD><TD> Include file for topology </TD></TR>
  42 <TR><TD ALIGN=RIGHT> <b><tt>-of</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">  freeze.ndx</a></tt> </TD><TD> Output, Opt. </TD><TD> Index file </TD></TR>
  43 </TABLE>
  44 <P>
  45 <H3>Other options</H3>
  46 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  47 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  48 <TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print help info and quit </TD></TD>
  49 <TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print version info and quit </TD></TD>
  50 <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>
  51 <TR><TD ALIGN=RIGHT> <b><tt>-fc</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>1000 1000 1000</tt> </TD><TD> Force constants (kJ/mol nm^2) </TD></TD>
  52 <TR><TD ALIGN=RIGHT> <b><tt>-freeze</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> If the <tt>-of</tt> option or this one is given an index file will be written containing atom numbers of all atoms that have a B-factor less than the level given here </TD></TD>
  53 <TR><TD ALIGN=RIGHT> <b><tt>-[no]disre</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Generate a distance restraint matrix for all the atoms in index </TD></TD>
  54 <TR><TD ALIGN=RIGHT> <b><tt>-disre_dist</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.1   </tt> </TD><TD> Distance range around the actual distance for generating distance restraints </TD></TD>
  55 <TR><TD ALIGN=RIGHT> <b><tt>-disre_frac</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Fraction of distance to be used as interval rather than a fixed distance. If the fraction of the distance that you specify here is less than the distance given in the previous option, that one is used instead. </TD></TD>
  56 <TR><TD ALIGN=RIGHT> <b><tt>-disre_up2</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1     </tt> </TD><TD> Distance between upper bound for distance restraints, and the distance at which the force becomes constant (see manual) </TD></TD>
  57 <TR><TD ALIGN=RIGHT> <b><tt>-cutoff</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1    </tt> </TD><TD> Only generate distance restraints for atoms pairs within cutoff (nm) </TD></TD>
  58 <TR><TD ALIGN=RIGHT> <b><tt>-[no]constr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Generate a constraint matrix rather than distance restraints. Constraints of type 2 will be generated that do generate exclusions. </TD></TD>
  59 </TABLE>
  60 <P>
  61 <hr>
  62 <div ALIGN=RIGHT>
  63 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
  64 <font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
  65 </div>
  66 </BODY>