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    On 29/02/2012 7:21 PM, aiswarya pawar wrote:
    <blockquote
cite="mid:CAEa6cRCMMGSv7a6qM3BYUCNvk968bp7Xn3xQ_NgEgCofK_wGxg@mail.gmail.com"
      type="cite">Mark,<br>
      <br>
      i want to know which water atoms stay within a cut off to protein
      atom.</blockquote>
    <br>
    OK, but as you will read in g_mindist -h, it will count such atoms
    and not identify which they were...<br>
    <br>
    <blockquote
cite="mid:CAEa6cRCMMGSv7a6qM3BYUCNvk968bp7Xn3xQ_NgEgCofK_wGxg@mail.gmail.com"
      type="cite"> ie i need the duration at which a water resides on
      the protein atoms.</blockquote>
    <br>
    ... and identity of the atoms is needed for measuring duration of
    contact. g_dist does something like this, and reading g_mindist -h
    should have prompted you to find this out.<br>
    <br>
    Otherwise, you will have to construct an index group for each water
    molecule, and script a loop to examine each water molecule
    separately using some tool that observes what you really want to
    measure.<br>
    <br>
    <blockquote
cite="mid:CAEa6cRCMMGSv7a6qM3BYUCNvk968bp7Xn3xQ_NgEgCofK_wGxg@mail.gmail.com"
      type="cite"> so for that i need the whole 5ns frames because am
      looking for water molecules which reside more than 50% of time.<br>
    </blockquote>
    <br>
    You also need to be clear about whether you care about continuous
    contact. Does a water molecule that oscillates at a distance around
    the cutoff reside about 50% of the time?<br>
    <br>
    You still don't need high time resolution for testing whether this
    analysis might give you the information you want. The water
    molecules that are in contact for more than 50% of the time
    (continuous or not) will show up in 5 snapsnots spaced every
    nanosecond. 5000 snapshots every picosecond is better, but not if
    you can't afford to wait for it.<br>
    <br>
    Mark<br>
    <br>
    <blockquote
cite="mid:CAEa6cRCMMGSv7a6qM3BYUCNvk968bp7Xn3xQ_NgEgCofK_wGxg@mail.gmail.com"
      type="cite">
      <br>
      Thanks<br>
      <br>
      <div class="gmail_quote">On Wed, Feb 29, 2012 at 12:41 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 6:01 PM, aiswarya pawar
              wrote:
              <blockquote type="cite">Mark,<br>
                <br>
                Right now am computing distance between each protein
                atom against all water atoms,</blockquote>
              <br>
            </div>
            That's expensive. mdrun goes to great lengths to speed up
            computing billions of distances. <br>
            <div class="im"> <br>
              <blockquote type="cite"> which is taking too long for 5ns
                run. i cant reduce the frames</blockquote>
              <br>
            </div>
            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.
            <div class="im"><br>
              <br>
              <blockquote type="cite"> either the number of water atoms.
                So is there any alternate.<br>
                <br>
              </blockquote>
              <br>
            </div>
            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".<span class="HOEnZb"><font color="#888888"><br>
                <br>
                Mark</font></span>
            <div class="im"><br>
              <br>
              <blockquote 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"
                      target="_blank">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> 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><font
                          color="#888888"><br>
                          <br>
                          Mark</font></span>
                      <div><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>
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                <br>
                -- <br>
                Aiswarya&nbsp; B Pawar<br>
                <br>
                <div> Project Assistant,<br>
                  Bioinformatics Dept, <br>
                  Indian Institute of Science<br>
                  Bangalore<br>
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      <br>
      -- <br>
      Aiswarya&nbsp; B Pawar<br>
      <br>
      <div>
        Project Assistant,<br>
        Bioinformatics Dept, <br>
        Indian Institute of Science<br>
        Bangalore<br>
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