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    On 29/02/2012 6:01 PM, aiswarya pawar wrote:
    <blockquote
cite="mid:CAEa6cRBCdTKfp_XdFEH8OZ2F==06JqoMWy3a6VUmhSBUuPzD9g@mail.gmail.com"
      type="cite">Mark,<br>
      <br>
      Right now am computing distance between each protein atom against
      all water atoms,</blockquote>
    <br>
    That's expensive. mdrun goes to great lengths to speed up computing
    billions of distances. <br>
    <br>
    <blockquote
cite="mid:CAEa6cRBCdTKfp_XdFEH8OZ2F==06JqoMWy3a6VUmhSBUuPzD9g@mail.gmail.com"
      type="cite"> which is taking too long for 5ns run. i cant reduce
      the frames</blockquote>
    <br>
    Yes you can. Even if you think you need data from every frame, you
    probably don't because they're correlated with each other, and at
    the very least you can do a pilot study on a frame every 100ps or
    every nanosecond before committing to one on all the frames.<br>
    <br>
    <blockquote
cite="mid:CAEa6cRBCdTKfp_XdFEH8OZ2F==06JqoMWy3a6VUmhSBUuPzD9g@mail.gmail.com"
      type="cite"> either the number of water atoms. So is there any
      alternate.<br>
      <br>
    </blockquote>
    <br>
    You are not likely to get a better solution if you only describe
    your attempt, rather than describe the objective. Asking "how do I
    hammer harder?" if you're hammering a screw makes it impossible to
    get the correct solution "Use a screwdriver".<br>
    <br>
    Mark<br>
    <br>
    <blockquote
cite="mid:CAEa6cRBCdTKfp_XdFEH8OZ2F==06JqoMWy3a6VUmhSBUuPzD9g@mail.gmail.com"
      type="cite">Thanks<br>
      <br>
      <div class="gmail_quote">On Wed, Feb 29, 2012 at 12:27 PM, Mark
        Abraham <span dir="ltr">&lt;<a moz-do-not-send="true"
            href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>&gt;</span>
        wrote:<br>
        <blockquote class="gmail_quote" style="margin:0pt 0pt 0pt
          0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
          <div bgcolor="#FFFFFF" text="#000000">
            <div class="im"> On 29/02/2012 5:17 PM, aiswarya pawar
              wrote:
              <blockquote type="cite">Dear all,<br>
                <br>
                Am running g_mindist on large number of atoms, i would
                like to know whether i can run this on more than one
                processors say 8 processors to speed up the task?</blockquote>
              <br>
            </div>
            No. If it will take too long, you need to reduce your number
            of frames (trjconv), or the number of atoms (also trjconv),
            or some such.<span class="HOEnZb"><font color="#888888"><br>
                <br>
                Mark</font></span>
            <div class="im"><br>
              <br>
              <blockquote type="cite"> and will this effect the output
                in anyways.<br>
                <br>
                Thanks,<br clear="all">
                <br>
                -- <br>
                Aiswarya&nbsp; B Pawar<br>
                <br>
                <br>
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          --<br>
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        </blockquote>
      </div>
      <br>
      <br clear="all">
      <br>
      -- <br>
      Aiswarya&nbsp; B Pawar<br>
      <br>
      <div>
        Project Assistant,<br>
        Bioinformatics Dept, <br>
        Indian Institute of Science<br>
        Bangalore<br>
        <br>
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