<html>
  <head>
    <meta content="text/html; charset=ISO-8859-1"
      http-equiv="Content-Type">
  </head>
  <body bgcolor="#FFFFFF" text="#000000">
    On 26/10/2011 7:54 PM, James Starlight wrote:
    <blockquote
cite="mid:CAALQopweJss8xE1eOSZYhUu+YtxeAsLk9U7YoXMk8zqKugqBQw@mail.gmail.com"
      type="cite">I've found that in general ussage of cutt-offs beetwen
      0.8-1.2 nm might provide good results.<br>
      <br>
      But now I have some problems with minimization of my initial
      structure<br>
      <br>
      Firstly, I've performed steep minimization ( emtool=1000,&nbsp;
      emstep&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; = 0.01 ) and than CG minimization (emtool=1,&nbsp;
      emstep&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; = 0.001) but as the result I've obtain that my
      struucture didnt minimize properly. <br>
      Is there any different strategies for the minimization for the ANM
      ?<br>
    </blockquote>
    <br>
    We don't know the sense in which it "didn't minimize properly," so
    there's not much point us guessing.<br>
    <br>
    <blockquote
cite="mid:CAALQopweJss8xE1eOSZYhUu+YtxeAsLk9U7YoXMk8zqKugqBQw@mail.gmail.com"
      type="cite"><br>
      In addition I'd like to know about conditions of such normal mode
      simulations. Does this procedure require in the PBC ? ( I've
      performed all steps including energy minimization in vacuu)<br>
    </blockquote>
    <br>
    Whether not PBC represents useful boundary conditions depends on
    what conditions you are trying to model - whether possible
    periodicity artefacts or boundary artefacts are more likely to
    affect your results.<br>
    <br>
    It does sound like you would benefit from reading some good textbook
    material on molecular simulation :)<br>
    <br>
    Mark<br>
    <br>
    <blockquote
cite="mid:CAALQopweJss8xE1eOSZYhUu+YtxeAsLk9U7YoXMk8zqKugqBQw@mail.gmail.com"
      type="cite">
      <br>
      <br>
      James<br>
      <br>
      <div class="gmail_quote">2011/10/25 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><br>
        <blockquote class="gmail_quote" style="margin:0 0 0
          .8ex;border-left:1px #ccc solid;padding-left:1ex;">
          <div text="#000000" bgcolor="#FFFFFF">
            <div class="im"> On 25/10/2011 3:30 AM, James Starlight
              wrote:
              <blockquote type="cite">I understand this but I've not
                been able found such information. I dont need in the
                most accurately&nbsp; parametries for all cutt-offs of my
                system but I want to gain inside into the basic cutt-
                offs worked with the Normal mode analysis.<br>
              </blockquote>
              <br>
            </div>
            The cut-offs are particular to the force field, not the
            manner in which the force field is used (EM vs MD vs
            whatever). There are literature references in the GROMACS
            manual, and also in the published work that you have been
            reading because it has objectives similar to yours. (hint,
            hint) <br>
            <div class="im"> <br>
              <blockquote type="cite"> <br>
                E.g I've found that PME is not worked here. </blockquote>
              <br>
            </div>
            PME does work here. Last time you were apparently
            mis-matching files...
            <div class="im"><br>
              <br>
              <blockquote type="cite">So I must to constrain my system
                with simplest cuttoffs. Could you provide me with the
                simple example e.g cutt of for interaction beetwen
                C-alpha atoms only etc? <br>
              </blockquote>
              <br>
            </div>
            You can't do that, and shouldn't even if you could.<br>
            <font color="#888888"> <br>
              Mark</font>
            <div class="im"><br>
              <br>
              <blockquote type="cite"><br>
                James<br>
                <br>
                <div class="gmail_quote"><br>
                  <blockquote class="gmail_quote" style="margin:0 0 0
                    .8ex;border-left:1px #ccc solid;padding-left:1ex">
                    <div text="#000000" bgcolor="#FFFFFF">
                      <div> <br>
                      </div>
                      These are particular to the force field involved,
                      not the software. Please consult the appropriate
                      literature, and see what others have used for
                      similar work.
                      <div><br>
                      </div>
                    </div>
                  </blockquote>
                </div>
              </blockquote>
              <br>
            </div>
          </div>
          <br>
          --<br>
          gmx-users mailing list &nbsp; &nbsp;<a moz-do-not-send="true"
            href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
          <a moz-do-not-send="true"
            href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
            target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
          Please search the archive at <a moz-do-not-send="true"
            href="http://www.gromacs.org/Support/Mailing_Lists/Search"
            target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
          before posting!<br>
          Please don't post (un)subscribe requests to the list. Use the<br>
          www interface or send it to <a moz-do-not-send="true"
            href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
          Can't post? Read <a moz-do-not-send="true"
            href="http://www.gromacs.org/Support/Mailing_Lists"
            target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
        </blockquote>
      </div>
      <br>
      <br>
      <fieldset class="mimeAttachmentHeader"></fieldset>
      <br>
    </blockquote>
    <br>
  </body>
</html>