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    On 2/02/2012 12:28 AM, aiswarya pawar wrote:
    <blockquote
cite="mid:CAEa6cRAM_NxVOEx_0GgZSaMPh=ERa3GpcLcywnTjLbyn-egdYQ@mail.gmail.com"
      type="cite">Hi,<br>
      <br>
      I have used the command =<br>
      <br>
      g_dist -f md.xtc -s md.tpr -n index.ndx <br>
      <br>
      which gives an output of data=<br>
      <br>
      &nbsp; 0.0000000&nbsp;&nbsp;&nbsp; 0.6259024&nbsp;&nbsp;&nbsp; 0.3880000&nbsp;&nbsp;&nbsp; 0.3610001&nbsp;&nbsp; -0.3329997<br>
      &nbsp;&nbsp; 1.0000000&nbsp;&nbsp;&nbsp; 0.6778775&nbsp;&nbsp;&nbsp; 0.2590003&nbsp;&nbsp;&nbsp; 0.5939999&nbsp;&nbsp; -0.1989999<br>
      &nbsp;&nbsp; 2.0000000&nbsp;&nbsp;&nbsp; 0.6759030&nbsp;&nbsp;&nbsp; 0.2529998&nbsp;&nbsp;&nbsp; 0.5939999&nbsp;&nbsp; -0.2000003<br>
      &nbsp;&nbsp; 3.0000000&nbsp;&nbsp;&nbsp; 0.6463353&nbsp;&nbsp;&nbsp; 0.1690001&nbsp;&nbsp;&nbsp; 0.5680003&nbsp;&nbsp; -0.2579999<br>
      &nbsp;&nbsp; 4.0000000&nbsp;&nbsp;&nbsp; 0.6808891&nbsp;&nbsp;&nbsp; 0.2639999&nbsp;&nbsp;&nbsp; 0.6050000&nbsp;&nbsp; -0.1669998<br>
      &nbsp;&nbsp; 5.0000000&nbsp;&nbsp;&nbsp; 0.6883561&nbsp;&nbsp;&nbsp; 0.3090000&nbsp;&nbsp;&nbsp; 0.5920000&nbsp;&nbsp; -0.1670003<br>
      &nbsp;&nbsp; 6.0000000&nbsp;&nbsp;&nbsp; 0.6201660&nbsp;&nbsp;&nbsp; 0.2769997&nbsp;&nbsp;&nbsp; 0.5139999&nbsp;&nbsp; -0.2090001<br>
      &nbsp;&nbsp; 7.0000000&nbsp;&nbsp;&nbsp; 0.6832005&nbsp;&nbsp;&nbsp; 0.2910001&nbsp;&nbsp;&nbsp; 0.5809999&nbsp;&nbsp; -0.2110000<br>
      &nbsp;&nbsp; 8.0000000&nbsp;&nbsp;&nbsp; 0.6472999&nbsp;&nbsp;&nbsp; 0.2960002&nbsp;&nbsp;&nbsp; 0.5339999&nbsp;&nbsp; -0.2150002<br>
      &nbsp;&nbsp; 9.0000000&nbsp;&nbsp;&nbsp; 0.6542692&nbsp;&nbsp;&nbsp; 0.1880000&nbsp;&nbsp;&nbsp; 0.5400000&nbsp;&nbsp; -0.3180003<br>
      &nbsp; 10.0000000&nbsp;&nbsp;&nbsp; 0.6725602&nbsp;&nbsp;&nbsp; 0.3230002&nbsp;&nbsp;&nbsp; 0.5780001&nbsp;&nbsp; -0.1180000<br>
      &nbsp; 11.0000000&nbsp;&nbsp;&nbsp; 0.6138712&nbsp;&nbsp;&nbsp; 0.3470001&nbsp;&nbsp;&nbsp; 0.4769998&nbsp;&nbsp; -0.1700001<br>
      &nbsp; 12.0000000&nbsp;&nbsp;&nbsp; 0.6999645&nbsp;&nbsp;&nbsp; 0.2860000&nbsp;&nbsp;&nbsp; 0.6150002&nbsp;&nbsp; -0.1729999<br>
      &nbsp; 13.0000000&nbsp;&nbsp;&nbsp; 0.6504593&nbsp;&nbsp;&nbsp; 0.1200001&nbsp;&nbsp;&nbsp; 0.6160002&nbsp;&nbsp; -0.1710000<br>
      &nbsp; 14.0000000&nbsp;&nbsp;&nbsp; 0.6447160&nbsp;&nbsp;&nbsp; 0.2110000&nbsp;&nbsp;&nbsp; 0.5869999&nbsp;&nbsp; -0.1629996<br>
      &nbsp; 15.0000000&nbsp;&nbsp;&nbsp; 0.6645610&nbsp;&nbsp;&nbsp; 0.2040000&nbsp;&nbsp;&nbsp; 0.5710001&nbsp;&nbsp; -0.2720003<br>
      &nbsp; 16.0000000&nbsp;&nbsp;&nbsp; 0.6481276&nbsp;&nbsp;&nbsp; 0.2330003&nbsp;&nbsp;&nbsp; 0.5560002&nbsp;&nbsp; -0.2379999<br>
      &nbsp; 17.0000000&nbsp;&nbsp;&nbsp; 0.6511113&nbsp;&nbsp;&nbsp; 0.2240002&nbsp;&nbsp;&nbsp; 0.5609999&nbsp;&nbsp; -0.2430000<br>
      &nbsp; 18.0000000&nbsp;&nbsp;&nbsp; 0.7119258&nbsp;&nbsp;&nbsp; 0.2650001&nbsp;&nbsp;&nbsp; 0.6220002&nbsp;&nbsp; -0.2230000<br>
      &nbsp; 19.0000000&nbsp;&nbsp;&nbsp; 0.6653563&nbsp;&nbsp;&nbsp; 0.0929999&nbsp;&nbsp;&nbsp; 0.6170001&nbsp;&nbsp; -0.2309999<br>
      &nbsp; 20.0000000&nbsp;&nbsp;&nbsp; 0.6881638&nbsp;&nbsp;&nbsp; 0.2520001&nbsp;&nbsp;&nbsp; 0.6070004&nbsp;&nbsp; -0.2040000<br>
      &nbsp; 21.0000000&nbsp;&nbsp;&nbsp; 0.7161944&nbsp;&nbsp;&nbsp; 0.2090001&nbsp;&nbsp;&nbsp; 0.6220002&nbsp;&nbsp; -0.2870002<br>
      &nbsp; 22.0000000&nbsp;&nbsp;&nbsp; 0.6587778&nbsp;&nbsp;&nbsp; 0.1400001&nbsp;&nbsp;&nbsp; 0.6020002&nbsp;&nbsp; -0.2279997<br>
      &nbsp; 23.0000000&nbsp;&nbsp;&nbsp; 0.5798631&nbsp;&nbsp;&nbsp; 0.0170002&nbsp;&nbsp;&nbsp; 0.5160003&nbsp;&nbsp; -0.2639999<br>
      &nbsp; 24.0000000&nbsp;&nbsp;&nbsp; 0.5862564&nbsp;&nbsp;&nbsp; 0.0390000&nbsp;&nbsp;&nbsp; 0.5239997&nbsp;&nbsp; -0.2599998<br>
      &nbsp; 25.0000000&nbsp;&nbsp;&nbsp; 0.6923014&nbsp;&nbsp; -0.1240001&nbsp;&nbsp;&nbsp; 0.5520000&nbsp;&nbsp; -0.3990002<br>
      &nbsp; 26.0000000&nbsp;&nbsp;&nbsp; 0.5787479&nbsp;&nbsp; -0.0899997&nbsp;&nbsp;&nbsp; 0.5050001&nbsp;&nbsp; -0.2680001<br>
      &nbsp; 27.0000000&nbsp;&nbsp;&nbsp; 0.5776323&nbsp;&nbsp; -0.2589998&nbsp;&nbsp;&nbsp; 0.4730000&nbsp;&nbsp; -0.2070003<br>
      &nbsp; 28.0000000&nbsp;&nbsp;&nbsp; 0.5910018&nbsp;&nbsp; -0.1630001&nbsp;&nbsp;&nbsp; 0.5250001&nbsp;&nbsp; -0.2170000<br>
      &nbsp; 29.0000000&nbsp;&nbsp;&nbsp; 0.4448786&nbsp;&nbsp; -0.1570001&nbsp;&nbsp;&nbsp; 0.4020000&nbsp;&nbsp; -0.1079998<br>
      &nbsp; 30.0000000&nbsp;&nbsp;&nbsp; 0.4806164&nbsp;&nbsp; -0.2160001&nbsp;&nbsp;&nbsp; 0.4000001&nbsp;&nbsp; -0.1560001<br>
      &nbsp; 31.0000000&nbsp;&nbsp;&nbsp; 0.5405830&nbsp;&nbsp; -0.1700001&nbsp;&nbsp;&nbsp; 0.4730000&nbsp;&nbsp; -0.1989999<br>
      &nbsp; 32.0000000&nbsp;&nbsp;&nbsp; 0.5614526&nbsp;&nbsp; -0.1080003&nbsp;&nbsp;&nbsp; 0.4930000&nbsp;&nbsp; -0.2459998<br>
      &nbsp; 33.0000000&nbsp;&nbsp;&nbsp; 0.4994450&nbsp;&nbsp; -0.0730000&nbsp;&nbsp;&nbsp; 0.4500003&nbsp;&nbsp; -0.2040000<br>
      &nbsp; 34.0000000&nbsp;&nbsp;&nbsp; 0.5323368&nbsp;&nbsp; -0.1420002&nbsp;&nbsp;&nbsp; 0.4830003&nbsp;&nbsp; -0.1730003<br>
      <br>
      <br>
      From this the first column is the time and the second is the water
      protein atom distance. so when am using the g_analyze i would use
      the 1st and 2nd column for the input? More over now this distances
      are below 0.8 nm . what would i do if my data in between shows
      distance more than 0.8nm. <br>
    </blockquote>
    <br>
    The above command measures distances between centres of masses of
    groups, like g_dist -h says. It doesn't measure "distance between
    protein and water atoms within a cut off". You still haven't
    described what you're trying to measure, or what your simulation
    looks like, so it's impossible to help you.<br>
    <br>
    Mark<br>
    <br>
    <blockquote
cite="mid:CAEa6cRAM_NxVOEx_0GgZSaMPh=ERa3GpcLcywnTjLbyn-egdYQ@mail.gmail.com"
      type="cite">
      <br>
      Thanks<br>
      <div class="gmail_quote">On Wed, Feb 1, 2012 at 6:48 PM, Justin A.
        Lemkul <span dir="ltr">&lt;<a moz-do-not-send="true"
            href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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 class="im"><br>
            <br>
            aiswarya pawar wrote:<br>
            <blockquote class="gmail_quote" style="margin:0pt 0pt 0pt
              0.8ex;border-left:1px solid
              rgb(204,204,204);padding-left:1ex">
              Dear Gromacs Users,<br>
              <br>
              i have data for the distance between the protein and water
              atoms within a cut off of 8A for 5ns using the g_dist
              option. Now i want to use g_analyze on this data. The time
              frame in the output data is not continuous because of the
              cut off provided. So i would like to know how would the
              g_analyze would compute the data.<br>
              <br>
              <br>
            </blockquote>
            <br>
          </div>
          I'm not clear on what you're trying to do. &nbsp;g_analyze performs
          simple statistical operations (averages, error estimates) on
          the input data. &nbsp;If there are discontinuities (which I do not
          understand the nature of), they come from the g_dist data, not
          what g_analyze is doing.<br>
          <br>
          Please provide a more clear description of what you are doing,
          including all relevant commands, and examples of the data
          files, if necessary.<br>
          <br>
          -Justin<br>
          <br>
          --<br>
          ========================================<br>
          <br>
          Justin A. Lemkul<br>
          Ph.D. Candidate<br>
          ICTAS Doctoral Scholar<br>
          MILES-IGERT Trainee<br>
          Department of Biochemistry<br>
          Virginia Tech<br>
          Blacksburg, VA<br>
          jalemkul[at]<a moz-do-not-send="true" href="http://vt.edu"
            target="_blank">vt.edu</a> | (540) 231-9080<br>
          <a moz-do-not-send="true"
            href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
            target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
          <br>
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      </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>
      </div>
      <br>
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    </blockquote>
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