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    On 15/05/2011 12:01 AM, Sikandar Mashayak wrote:
    <blockquote
      cite="mid:BANLkTi=q7Wo7NSwW7jasLEq0N=KHMdTseA@mail.gmail.com"
      type="cite">Hey Mark
      <div><br>
      </div>
      <div>Do you mean removing all bond definitions from topology file,
        when you say well constructed topology to exclude all
        bonded-interactions in rerun?</div>
    </blockquote>
    <br>
    I said you can decompose the bonded interactions. You can have none
    by removing all bonded interactions, but that won't save you any
    significant time, nor serve any other purpose.<br>
    <br>
    Mark<br>
    <br>
    <blockquote
      cite="mid:BANLkTi=q7Wo7NSwW7jasLEq0N=KHMdTseA@mail.gmail.com"
      type="cite">
      <div><br>
      </div>
      <div>thanks</div>
      <div>sikandar</div>
      <div><br>
        <div class="gmail_quote">On Sat, May 14, 2011 at 8:01 AM, 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>
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            <div class="im">On 14/05/2011 10:52 PM, XAvier Periole
              wrote:<br>
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                <br>
                Two things you have to be careful about:<br>
                1- use trr trajectory files. xtc precision is not
                sufficient and it will give a lot of discrepancies at
                least for the bonded terms.<br>
                2- set the nstlist to 1 as the neiboring list should be
                undated for each frame and not every 5/10 as it is
                normally set in a regular mdp file.<br>
              </blockquote>
              <br>
            </div>
            Reruns do neighbour searching every frame, regardless.<br>
            <font color="#888888">
              <br>
              Mark</font>
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              <div class="h5"><br>
                <br>
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                  <br>
                  On May 14, 2011, at 1:11 PM, Justin A. Lemkul wrote:<br>
                  <br>
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                    <br>
                    <br>
                    Ramachandran G wrote:<br>
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                      Hello gmx users:<br>
                      &nbsp; &nbsp; I did 1ns simulation for my system and have
                      the trajectory and energy files.<br>
                      Now i want to see the energy of some specific
                      residues. So, i decompose(separated) the energy
                      groups and edited the mdp file.<br>
                      Using the mdp file, i created a new tpr file and
                      rerun the mdrun using the trajectory file. But
                      when i compared the total energy between the old
                      and new one, it differs a lot.<br>
                      I am doing some mistakes somewhere. Can anyone
                      help me please. Thanks.<br>
                    </blockquote>
                    <br>
                    Maybe, maybe not. &nbsp;Without seeing the .mdp settings
                    and the data that you're looking at, all anyone can
                    do is guess. &nbsp;You also haven't stated what type of
                    trajectory (i.e. .xtc or .trr) you're using as
                    -rerun input. &nbsp;If you're using an .xtc file, there
                    is no velocity information, so any property related
                    to velocities (most notably kinetic energy, but
                    several others as well) will be zero. &nbsp;I suspect
                    this is probably where the discrepancy is, but it is
                    not a problem. &nbsp;Using energygrps is only useful for
                    decomposing short-range nonbonded energy terms,
                    nothing else.<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> |
                    <a moz-do-not-send="true"
                      href="tel:%28540%29%20231-9080"
                      value="+15402319080" target="_blank">(540)
                      231-9080</a><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>
                    ========================================<br>
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