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    On 19/02/2011 5:18 PM, C.Y. Chang wrote:
    <blockquote
      cite="mid:AANLkTi=DAAvyk-bS1Wa6=sZSROX8vmNw_711kR-a3m6U@mail.gmail.com"
      type="cite">Hi,<br>
      <br>
      The errpr msg. that I expressed in the previous mail is unclear.<br>
      It really happened in the grompp step of my dealinw with the em.<br>
      The manual shows that the viste can be used by <br>
      <br>
      [ virtual sites2 ]<br>
    </blockquote>
    <br>
    That's misspelled too. Underscores are significant. You have to be
    literal when dealing with computers.<br>
    <br>
    <blockquote
      cite="mid:AANLkTi=DAAvyk-bS1Wa6=sZSROX8vmNw_711kR-a3m6U@mail.gmail.com"
      type="cite">
      ; Site from funct a<br>
      5 1 2 1 0.7439756<br>
      <br>
      What should I choose the vsite for the -CN group? (2, 3fd or
      others?)<br>
    </blockquote>
    <br>
    The problems come when the force from normal angle and dihedral
    functions aren't numerically stable when there are 3 collinear
    atoms. The way to avoid this is to have one of those atoms
    "virtual". Forces on it get projected onto the real atoms from which
    it is defined, the integration of forces proceeds only on the real
    atoms, and the position of the virtual site gets reconstructed
    later. So, which type do you think will work best here?<br>
    <br>
    <blockquote
      cite="mid:AANLkTi=DAAvyk-bS1Wa6=sZSROX8vmNw_711kR-a3m6U@mail.gmail.com"
      type="cite">I read the manual and the columns of the vsite need
      some parameters.<br>
      The "Site" seems to be the atom number.<br>
    </blockquote>
    <br>
    Yes.<br>
    <br>
    <blockquote
      cite="mid:AANLkTi=DAAvyk-bS1Wa6=sZSROX8vmNw_711kR-a3m6U@mail.gmail.com"
      type="cite">
      The "from" seems some atom group, but which atoms should be
      included?<br>
    </blockquote>
    <br>
    The real atoms that form the virtual site. The number and order
    depends on the type of virtual site. Which atom is which is covered
    back in 4.7 You need to read that together with 5.2.2, like I said
    several emails ago.<br>
    <br>
    <blockquote
      cite="mid:AANLkTi=DAAvyk-bS1Wa6=sZSROX8vmNw_711kR-a3m6U@mail.gmail.com"
      type="cite">How could obtain the "func" values?<br>
    </blockquote>
    <br>
    That's situation-dependent. Here, you want to pick a position along
    the line that will lead to the three atoms being a sensible distance
    apart.<br>
    <br>
    <blockquote
      cite="mid:AANLkTi=DAAvyk-bS1Wa6=sZSROX8vmNw_711kR-a3m6U@mail.gmail.com"
      type="cite">Could you give me a molecule for my example?<br>
    </blockquote>
    <br>
    No, I don't have one. Your example above will construct atom 5 from
    1 and 2 75% of the way along the line from 1 to 2, per Figure 4.16
    and equation 4.134.<br>
    <br>
    Mark<br>
    <br>
    <blockquote
      cite="mid:AANLkTi=DAAvyk-bS1Wa6=sZSROX8vmNw_711kR-a3m6U@mail.gmail.com"
      type="cite">Thanks for your help.<br>
      <br>
      Best,<br>
      <br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Chia-yun<br>
      <br>
      <br>
      <div class="gmail_quote">2011/2/19 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: 0pt 0pt 0pt
          0.8ex; border-left: 1px solid rgb(204, 204, 204);
          padding-left: 1ex;">
          <div text="#000000" bgcolor="#ffffff">
            <div class="im"> On 19/02/2011 3:02 PM, C.Y. Chang wrote: </div>
            <blockquote type="cite">Hi,<br>
              <br>
              <div class="im"> I have tried to add<br>
                <br>
                [ position restraints ]<br>
              </div>
            </blockquote>
            <br>
            This is misspelled. Surely grompp warned about this?
            <div class="im"><br>
              <br>
              <blockquote type="cite">2 1 1000 1000 1000 ; Restrain to a
                point<br>
                1 1 1000 0 1000 ; Restrain to a line (Y-axis)<br>
                3 1 1000 0 0 ; Restrain to a plane (Y-Z-plane)<br>
                <br>
                in the end of the topology file.<br>
              </blockquote>
              <br>
            </div>
            This does not even approach the solution to your problem.
            Position restraints inhibit diffusion and structural
            changes. You need a vsite, like you knew earlier.
            <div class="im"><br>
              <br>
              <blockquote type="cite">In the em. process, I get the
                eroor msg.<br>
              </blockquote>
              <br>
            </div>
            No, this error happened in grompp.
            <div class="im"><br>
              <br>
              <blockquote type="cite">Fatal error:<br>
                Invalid dihedral type 1000<br>
              </blockquote>
              <br>
            </div>
            GROMACS didn't recognise the mis-spelled directive, and so
            it's trying to make sense of your position restraint lines
            as dihedrals.<br>
            <font color="#888888"> <br>
              Mark</font>
            <div>
              <div class="h5"><br>
                <br>
                <blockquote type="cite">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
                  Chia-yun<br>
                  <br>
                  <br>
                  <div class="gmail_quote">2011/2/18 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><br>
                    <blockquote class="gmail_quote" style="margin: 0pt
                      0pt 0pt 0.8ex; border-left: 1px solid rgb(204,
                      204, 204); padding-left: 1ex;">
                      <div>On 18/02/2011 1:13 PM, C.Y. Chang wrote:<br>
                        <blockquote class="gmail_quote" style="margin:
                          0pt 0pt 0pt 0.8ex; border-left: 1px solid
                          rgb(204, 204, 204); padding-left: 1ex;"> Hi,<br>
                          <br>
                          I am dealing with the lipid bilayer permeation
                          simulation.<br>
                          Most compounds can be finished, but the
                          compounds with CN can't be performed
                          simulation.<br>
                          I have searched the discussion in the
                          gmx-users discussion.<br>
                          The "vsite" has been mentioned, and I have
                          refered to the gromacs manual.<br>
                          But I don't understand that how I can use the
                          "vsite".<br>
                        </blockquote>
                        <br>
                      </div>
                      The theory is discussed in chapter 4 and there's a
                      brief example in 5.2.2. What have you tried and
                      what went wrong?<br>
                      <br>
                      Mark
                      <div>
                        <div><br>
                          <br>
                          <blockquote class="gmail_quote" style="margin:
                            0pt 0pt 0pt 0.8ex; border-left: 1px solid
                            rgb(204, 204, 204); padding-left: 1ex;">
                            (add the toplogy file or use the command
                            line?)<br>
                            I attach the PDB and toplogy file of the
                            molecule.<br>
                            First, I performed the molecular dynamic
                            simulation for the pure lipid bilayer, and
                            the step was been finished.<br>
                            After I insert the molecule, these command
                            lines are performed.<br>
                            <br>
                            grompp -f minim.mdp -c cmplx.pdb -p
                            topol_dppc.top -o em.tpr<br>
                            mdrun -v -deffnm em<br>
                            grompp -f npt_cmplx.mdp -c em.gro -p
                            topol_dppc.top -o npt_cmplx.tpr<br>
                            nohup mdrun -v -deffnm npt_cmplx &amp;<br>
                            <br>
                            Thanks for your help.<br>
                            Best,<br>
                            <br>
                            &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                            &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Chia-yun<br>
                          </blockquote>
                          <br>
                        </div>
                      </div>
                      <font color="#888888"> -- <br>
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