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    On 13/03/2012 1:13 AM, James Starlight wrote:
    <blockquote
cite="mid:CAALQopy9xW_T3_ys2Kr_JpaKPmV77Fxw1aOQ=-L-o0XVgTyWZg@mail.gmail.com"
      type="cite">Francesca,<br>
      <br>
      Yes I suppose this is good aproach for the generation of position
      restricktions on the desired atoms. But I want to restrain the
      distance between selected pairs of atoms ( e.g between C-alpha-
      C-alpha atoms of two different residues).<br>
    </blockquote>
    <br>
    The help for genrestr -disre says that this is exactly what it
    does... use an index group to make distance restraints.<br>
    <br>
    <blockquote
cite="mid:CAALQopy9xW_T3_ys2Kr_JpaKPmV77Fxw1aOQ=-L-o0XVgTyWZg@mail.gmail.com"
      type="cite">
      <br>
      Also I want to restrain some dihedral angles in the desired
      rotameric forms.<br>
      <br>
      In literature I've found that peple have dome the same things in
      Gromacs but I could not find detailed algorithm of such
      methodology :(<br>
    </blockquote>
    <br>
    There can't be a walk-through of everything anybody might ever do,
    unfortunately. Manual chapter 4 talks about the functional forms
    available. There's a table in section 5.5 that describes how to
    construct the line of a [ moleculetype ] section. That's all you
    need to know if have a general understanding of how the .top file
    works (elsewhere in chapter 5).<br>
    <br>
    Mark<br>
    <br>
    <blockquote
cite="mid:CAALQopy9xW_T3_ys2Kr_JpaKPmV77Fxw1aOQ=-L-o0XVgTyWZg@mail.gmail.com"
      type="cite">
      <br>
      James<br>
      <br>
      <div class="gmail_quote">12 &#1084;&#1072;&#1088;&#1090;&#1072; 2012&nbsp;&#1075;. 18:05 &#1087;&#1086;&#1083;&#1100;&#1079;&#1086;&#1074;&#1072;&#1090;&#1077;&#1083;&#1100;
        francesca vitalini <span dir="ltr">&lt;<a
            moz-do-not-send="true"
            href="mailto:francesca.vitalini11@gmail.com">francesca.vitalini11@gmail.com</a>&gt;</span>
        &#1085;&#1072;&#1087;&#1080;&#1089;&#1072;&#1083;:<br>
        <blockquote class="gmail_quote" style="margin:0pt 0pt 0pt
          0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">I
          think you can make an index file using make_ndx where you
          specify<br>
          the atoms you want to restraint.<br>
          Hope this can help.<br>
          Francesca<br>
          <br>
          2012/3/12 James Starlight &lt;<a moz-do-not-send="true"
            href="mailto:jmsstarlight@gmail.com">jmsstarlight@gmail.com</a>&gt;:<br>
          <div class="HOEnZb">
            <div class="h5">&gt; Dear Gromacs users!<br>
              &gt;<br>
              &gt;<br>
              &gt; I want to perform constrained MD simulation of my
              protein with inclusion of<br>
              &gt; some experimental restraints.<br>
              &gt;<br>
              &gt;<br>
              &gt; 1) I found that genrest cpmmand could be usefull for
              the generation of the<br>
              &gt; distance restrictions wich I could use in my
              constrined simulation.<br>
              &gt;<br>
              &gt; Also in manual I've found that command like<br>
              &gt;<br>
              &gt; genrestr -f b2ar.gro -disre -index.ndx -o test.itp<br>
              &gt;<br>
              &gt; will produce some distance restricted matrix of the
              whole groups presented<br>
              &gt; in the index.ndx file.<br>
              &gt;<br>
              &gt; So how I could select to contrain selected residues
              within selected distance<br>
              &gt; by means the index file?&nbsp; E.g I've manually point out
              2 residues in<br>
              &gt; index.ndx. I waant to preserve between that residues
              some desired distance D<br>
              &gt; wich I've obtaine from the experimental data. How I
              could do it via genrestr<br>
              &gt; and waht addition flags should I use for that purpose
              ?<br>
              &gt;<br>
              &gt;<br>
              &gt; 2) Is there any way to apply gradually the desired
              dist.resrs during MDrun<br>
              &gt; to prevent some artifacts in my system wich would
              occur due to the rapid<br>
              &gt; application of the dis.res ( e.g in cases where the
              conformation of the<br>
              &gt; started structure and that wich I'd obtained fter
              application of the<br>
              &gt; restrains are slightly different)?<br>
              &gt;<br>
              &gt; Thanks for help,<br>
              &gt;<br>
              &gt;<br>
              &gt; James<br>
              &gt;<br>
            </div>
          </div>
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