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    On 25/11/2011 6:38 PM, James Starlight wrote:
    <blockquote
cite="mid:CAALQopzn9bvRo13V85rA2skS53LBm2du_h1WKNo9E9Bz8kq6Hw@mail.gmail.com"
      type="cite">Mark, <span class="gD" style="color: rgb(121, 6,
        25);">Tsjerk thanks!<br>
        <br>
        I've check my uncompleated produced MD run by G_energy and find
        that average pressure is 1.1 Bar that is most close to ref.<br>
        <br>
        <br>
        By the way could you tell me about extra possible ways of
        checking running simmulation? ( E.g I'm calculating long produce
        trajectory and want to check my uncompleated system ).<br>
        <br>
        As I understood One of the possible way is the ussage of
        G_energy but how I could obtain GRO and TPR file from
        uncompleated MD trajectory ( .trr) (recently I've asked about
        this but I've missed that topic ;o)&nbsp; ?<br>
      </span></blockquote>
    <br>
    Choose a length of time in advance that you are happy to risk being
    wasted. Run that length of time, make a backup, check whatever you
    want to check, then continue the simulation. As you acquire
    confidence, you will want to increase that time (and like everyone
    you will regret that decision at least once!)<br>
    <br>
    Mark<br>
    <br>
    <blockquote
cite="mid:CAALQopzn9bvRo13V85rA2skS53LBm2du_h1WKNo9E9Bz8kq6Hw@mail.gmail.com"
      type="cite"><span class="gD" style="color:#790619">
        <br>
        <br>
        <br>
        Thanks again<br>
        <br>
        James<br>
      </span><br>
      <div class="gmail_quote">2011/11/25 Tsjerk Wassenaar <span
          dir="ltr">&lt;<a moz-do-not-send="true"
            href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>&gt;</span><br>
        <blockquote class="gmail_quote" style="margin:0 0 0
          .8ex;border-left:1px #ccc solid;padding-left:1ex;">
          <p>Hi James,</p>
          <p>There have been extensive discussions about this on the
            list. Check the archives. In short, smaller systems give
            larger fluctuations, and shorter simulations give larger
            deviations from the expected average.</p>
          <p>Cheers,</p>
          <p>Tsjerk</p>
          <font color="#888888">
          </font>
          <blockquote type="cite">
            <div>
              <div class="h5">On Nov 25, 2011 7:23 AM, "James Starlight"
                &lt;<a moz-do-not-send="true"
                  href="mailto:jmsstarlight@gmail.com" target="_blank">jmsstarlight@gmail.com</a>&gt;
                wrote:<br>
                <br>
                Dear Gromacs Users!<br>
                <br>
                <br>
                At the present time I'm simulating small peptide (11 a.c
                in coiled conformation) in water.<br>
                <br>
                I've desided to use parameters from Lysozyme simmulation
                ( opls ff for parametrisation and all mdp parameters
                from that simulation).<br>
                <br>
                Because my peptide was smaller than typical globular
                protein I've desided to use bigger periodical box than
                in tutorial<br>
                <br>
                I've used editconf&nbsp; -c -d 1.5 -bt cubic instead of 1.0
                nm in tutorial wich resulted in bigger box relative
                peptide size.<br>
                <br>
                so i have this box vectors &nbsp;&nbsp; 5.39318&nbsp;&nbsp; 5.39318&nbsp;&nbsp;
                5.39318<br>
                <br>
                My experiment was in full agreement with the above
                tutorial until NVP phase was conducted. I have conducted
                100ps equilibration but When I've checked average
                pressure it was 0.75 atm instead of 1 BAR and have big
                RMSD- 200. (also I've checked my system visually but it
                looks fine- I have not&nbsp; pointed any artifacts linked
                with unstable pressure like voids in the solvent etc).
                Should I equilibrate my sustem longer until pressure
                would not be stabilized to reference BAR?&nbsp; What another
                options should i take into account during simulation of
                the small peptides ?<br>
                <br>
                Thanks,<br>
                <br>
                James<br>
                <br>
              </div>
            </div>
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