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    On 21/01/2012 12:40 AM, Kiwoong Kim wrote:
    <blockquote
cite="mid:CALmcptC2otCCaTN9-c_aL6p4hm9HEK6e-sneunmZK2f6Sbbd6w@mail.gmail.com"
      type="cite">
      <div>Hi, Mark.</div>
      <div>&nbsp;</div>
      <div>I'am very grateful to your reply.</div>
      <div>&nbsp;</div>
      <div>I'm sorry not to keep the archive. Actually, I didn't know
        how to directly append the reply to the original post because I
        posted the previous&nbsp;question under the disabled-subscribed
        status.&nbsp;I haven't found the way to post the&nbsp;reply such status so
        far. </div>
      <div>&nbsp;</div>
      <div>I will try to model N2&nbsp;like you did mention. (two N atom
        (Atom type: A), Dummy single N2 molecule (Atom type: V) between
        N atoms) </div>
      <div>&nbsp;</div>
      <div>When I modeled&nbsp;CO2 (linear rigid body), I used below manner.
        &nbsp;</div>
      <div>&nbsp;</div>
      <div>&nbsp;&gt; [ atomtypes ]<br>
        &gt; ;&nbsp;&nbsp; type&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; mass&nbsp;&nbsp;&nbsp; charge&nbsp;&nbsp;&nbsp; ptype&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; c6&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
        c12<br>
        &gt;&nbsp;&nbsp;&nbsp;&nbsp; D1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 22.004975&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.0000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; A&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
        0.0000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.00000000<br>
        &gt;&nbsp;&nbsp;&nbsp;&nbsp; D2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 22.004975&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.0000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; A&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
        0.0000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.00000000<br>
        &gt;&nbsp;&nbsp;&nbsp;&nbsp; C_CO&nbsp;&nbsp;&nbsp;&nbsp; 0.0000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.5406&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; V&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
        0.0000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.00000000<br>
        &gt;&nbsp;&nbsp;&nbsp;&nbsp; O_CO&nbsp;&nbsp;&nbsp;&nbsp; 0.0000000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -0.2703&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; V&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
        0.29847&nbsp;&nbsp; 1.10765301<br>
        &gt; <br>
        &gt; [ moleculetype ]<br>
        &gt; ; name&nbsp; nrexcl<br>
        &gt; CO2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2<br>
        &gt; <br>
        &gt; [ atoms ]<br>
        &gt; ;&nbsp;&nbsp; nr&nbsp; type&nbsp;&nbsp;&nbsp; resnr&nbsp;&nbsp; residu&nbsp; atom&nbsp;&nbsp;&nbsp; cgnr&nbsp;&nbsp;&nbsp;
        charge&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; mass<br>
        &gt; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; D1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; CO2&nbsp;&nbsp;&nbsp; DUM&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.0000&nbsp;
        22.004975<br>
        &gt; 2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; D2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; CO2&nbsp;&nbsp;&nbsp; DUM&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.0000&nbsp;
        22.004975<br>
      </div>
    </blockquote>
    <br>
    Here the two dummy atoms are used to give the rigid CO2 the moments
    of inertia of a diatomic molecule. Whether that's reasonable would
    have to be seen in the results there... <br>
    <br>
    Mark<br>
    <br>
    <blockquote
cite="mid:CALmcptC2otCCaTN9-c_aL6p4hm9HEK6e-sneunmZK2f6Sbbd6w@mail.gmail.com"
      type="cite">
      <div>
        &gt; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C_CO&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; CO2&nbsp;&nbsp;&nbsp; C_CO&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.5406&nbsp;
        0.0000000<br>
        &gt; 4&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; O_CO&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; CO2&nbsp;&nbsp;&nbsp; O_CO&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -0.2703&nbsp;
        0.0000000<br>
        &gt; 5&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; O_CO&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; CO2&nbsp;&nbsp;&nbsp; O_CO&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -0.2703&nbsp;
        0.0000000<br>
        &gt; <br>
        &gt; [ constraints ]<br>
        &gt; ;&nbsp; ai&nbsp; aj funct&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; c0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; c1<br>
        &gt; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.2006146447<br>
        &gt; <br>
        &gt; [ virtualsites2]<br>
        &gt; ;&nbsp; ai&nbsp;&nbsp;&nbsp; aj&nbsp;&nbsp;&nbsp; ak&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; funct&nbsp;&nbsp; c0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; c1<br>
        &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.4263443<br>
        &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 4&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -0.07365569<br>
        &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.926344308<br>
        &gt; <br>
        &gt; [ exclusions ]<br>
        &gt; 4 3 5<br>
        &gt; 5 3 4<br>
        &gt; 3 5 4<br>
      </div>
      <div>Thanks Mark again. :)</div>
      <div>
        &nbsp;</div>
      <div>Have a great day.<br>
      </div>
      <div class="gmail_quote">2012/1/20 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 style="margin:0px 0px 0px
0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid"
          class="gmail_quote">
          <div text="#000000" bgcolor="#FFFFFF"> On 21/01/2012 12:04 AM,
            Kiwoong Kim wrote:
            <blockquote type="cite">
              <div style="background:white"><span
                  style="word-wrap:break-word" lang="EN-US">
                  <div>&nbsp;</div>
                  <p
style="background:white;width:100%;text-align:left;word-break:break-all;word-wrap:break-word"
                    class="MsoNormal" align="left"> </p>
                  <p><span lang="EN-US"> Hi,</span></p>
                  <p><span lang="EN-US"></span></p>
                </span></div>
            </blockquote>
            <br>
            Please do keep the discussion on the list, so others can
            learn and contribute now and from the archives.
            <div class="im"><br>
              <br>
              <blockquote type="cite">
                <div style="background:white"><span
                    style="word-wrap:break-word" lang="EN-US">
                    <p>&nbsp;</p>
                    <p
style="background:white;width:100%;text-align:left;word-break:break-all;word-wrap:break-word"
                      class="MsoNormal" align="left"><span lang="EN-US">I
                        don</span><span>&#8217;<span
                          style="word-break:break-all;word-wrap:break-word"
                          lang="EN-US">t know how to model N2 molecule
                          yet.</span></span></p>
                    <p
style="background:white;width:100%;text-align:left;word-break:break-all;word-wrap:break-word"
                      class="MsoNormal" align="left"><span lang="EN-US">
                      </span></p>
                    <p
style="background:white;width:100%;text-align:left;word-break:break-all;word-wrap:break-word"
                      class="MsoNormal" align="left"> <span
                        lang="EN-US">If I use virtual site for N2 model,
                        then, this can be done like below.</span></p>
                    <p
style="background:white;width:100%;text-align:left;word-break:break-all;word-wrap:break-word"
                      class="MsoNormal" align="left"> <span
                        lang="EN-US"> </span></p>
                    <p
style="background:white;width:100%;text-align:left;word-break:break-all;word-wrap:break-word"
                      class="MsoNormal" align="left"><span lang="EN-US">Hence,

                        where do I have to apply plus charge for making
                        N2 neutral??</span></p>
                    <p
style="background:white;width:100%;text-align:left;word-break:break-all;word-wrap:break-word"
                      class="MsoNormal" align="left"><span lang="EN-US">Can
                        it be D1 and D2 for plus charge?? </span></p>
                  </span></div>
              </blockquote>
              <br>
            </div>
            Why are you creating two dummy atoms? Your earlier post
            implied two negatively charged N atoms and a single (axial)
            positively-charged massless dummy atom would be an adequate
            model. The two N atoms have a bond or constraint between
            them, and the dummy atom is a type 2 virtual site half-way
            between them. IIRC this should be the same for linear rigid
            CO2, except that there the central particle has mass and
            charge.<span class="HOEnZb"><font color="#888888"><br>
                <br>
                Mark</font></span>
            <div>
              <div class="h5"><br>
                <br>
                <blockquote type="cite">
                  <div style="background:white"><span
                      style="word-break:break-all;word-wrap:break-word"
                      lang="EN-US">
                      <p
style="background:white;width:100%;text-align:left;word-break:break-all;word-wrap:break-word"
                        class="MsoNormal" align="left"> <span
                          lang="EN-US"> </span></p>
                      <p
style="background:white;width:100%;text-align:left;word-break:break-all;word-wrap:break-word"
                        class="MsoNormal" align="left"><span
                          lang="EN-US">Thx. </span></p>
                      <p
style="background:white;width:100%;text-align:left;word-break:break-all;word-wrap:break-word"
                        class="MsoNormal" align="left"> <span
                          lang="EN-US"> </span></p>
                      <p
style="background:white;width:100%;text-align:left;word-break:break-all;word-wrap:break-word"
                        class="MsoNormal" align="left"><span
                          lang="EN-US">[ atomtypes ]</span></p>
                      <p
style="background:white;width:100%;text-align:left;word-break:break-all;word-wrap:break-word"
                        class="MsoNormal" align="left"> <span
                          lang="EN-US">; type mass charge ptype sigma
                          epsilon</span></p>
                      <p
style="background:white;width:100%;text-align:left;word-break:break-all;word-wrap:break-word"
                        class="MsoNormal" align="left"> <span
                          lang="EN-US"> D1 14.00674 0.0000 A 0.0000
                          0.00000000</span></p>
                      <p
style="background:white;width:100%;text-align:left;word-break:break-all;word-wrap:break-word"
                        class="MsoNormal" align="left"> <span
                          lang="EN-US"> D2 14.00674 0.0000 A 0.0000
                          0.00000000</span></p>
                      <p
style="background:white;width:100%;text-align:left;word-break:break-all;word-wrap:break-word"
                        class="MsoNormal" align="left"> <span
                          lang="EN-US"> N 0.0000000 -0.4048 V 0.332
                          0.3026</span></p>
                      <pre style="background:white"><span style="word-break:break-all;word-wrap:break-word" lang="EN-US"> </span></pre>
                      <pre style="background:white"><span style="word-break:break-all;word-wrap:break-word" lang="EN-US"> [ moleculetype ]</span></pre>
                      <pre style="background:white"><span style="word-break:break-all;word-wrap:break-word" lang="EN-US"> ; name  nrexcl</span></pre>
                      <pre style="background:white"><span style="word-break:break-all;word-wrap:break-word" lang="EN-US"> N2         2</span></pre>
                      <pre style="background:white"><span style="word-break:break-all;word-wrap:break-word" lang="EN-US"> </span></pre>
                      <pre style="background:white"><span style="word-break:break-all;word-wrap:break-word" lang="EN-US"> [ atoms ]</span></pre>
                      <pre style="background:white"><span style="word-break:break-all;word-wrap:break-word" lang="EN-US"> ;   nr  type    resnr   residu  atom    cgnr    charge        mass</span></pre>
                      <pre style="background:white"><span style="word-break:break-all;word-wrap:break-word" lang="EN-US"> 1       D1       1       N2    D1       1        0.0000  14.00674</span></pre>
                      <pre style="background:white"><span style="word-break:break-all;word-wrap:break-word" lang="EN-US"> 2       D2       1       N2    D2       1        0.0000  14.00674</span></pre>
                      <pre style="background:white"><span style="word-break:break-all;word-wrap:break-word" lang="EN-US"> 3       N        1       N2    N        1       -0.4048  0.0000000</span></pre>
                      <pre style="background:white"><span style="word-break:break-all;word-wrap:break-word" lang="EN-US"> 4       N        1       N2    N        1       -0.4048  0.0000000</span></pre>
                      <pre style="background:white"><span style="word-break:break-all;word-wrap:break-word" lang="EN-US"> </span></pre>
                      <pre style="background:white;text-indent:12pt"><span style="word-break:break-all;word-wrap:break-word" lang="EN-US">[ constraints ]</span></pre>
                      <pre style="background:white"><span style="word-break:break-all;word-wrap:break-word" lang="EN-US"> ;  ai  aj funct           c0           c1</span></pre>
                      <pre style="background:white"><span style="word-break:break-all;word-wrap:break-word" lang="EN-US"> 1       2     1          0.1098</span></pre>
                      <pre style="background:white"><span style="word-break:break-all;word-wrap:break-word" lang="EN-US"> </span></pre>
                      <pre style="background:white"><span style="word-break:break-all;word-wrap:break-word" lang="EN-US"> [ virtualsites2]</span></pre>
                      <pre style="background:white"><span style="word-break:break-all;word-wrap:break-word" lang="EN-US"> ;  ai    aj    ak       funct   c0      c1</span></pre>
                      <pre style="background:white"><span style="word-break:break-all;word-wrap:break-word" lang="EN-US">      3     1     2       1       -0.5</span></pre>
                      <pre style="background:white"><span style="word-break:break-all;word-wrap:break-word" lang="EN-US">      4     1     2       1        0.5</span></pre>
                      <pre style="background:white"><span style="word-break:break-all;word-wrap:break-word" lang="EN-US"> </span></pre>
                      <pre style="background:white"><span style="word-break:break-all;word-wrap:break-word" lang="EN-US"> [ exclusions ]</span></pre>
                      <pre style="background:white"><span style="word-break:break-all;word-wrap:break-word" lang="EN-US">3 4</span></pre>
                      <div style="background:white"><span
                          style="word-break:break-all;word-wrap:break-word"
                          lang="EN-US">4 3</span></div>
                    </span></div>
                  <div style="background:white"><span
                      style="word-break:break-all;word-wrap:break-word"
                      lang="EN-US"></span>&nbsp;</div>
                  <div style="background:white"><span
                      style="word-break:break-all;word-wrap:break-word"
                      lang="EN-US"></span>&nbsp;</div>
                  <div style="background:white"><span
                      style="word-break:break-all;word-wrap:break-word"
                      lang="EN-US"></span>&nbsp;</div>
                  <div style="background:white"><span
                      style="word-break:break-all;word-wrap:break-word"
                      lang="EN-US">Below is the previous post message</span></div>
                  <div style="background:white"><span
                      style="word-break:break-all;word-wrap:break-word"
                      lang="EN-US"></span> </div>
                  <div style="background:white"><span
                      style="word-break:break-all;word-wrap:break-word"
                      lang="EN-US">
                      <pre style="margin:0em">On 20/01/2012 5:51 PM, Kiwoong Kim wrote:
</pre>
                      <blockquote
style="margin:0em;padding-left:0.85em;border-left-color:rgb(85,85,238);border-left-width:0.2em;border-left-style:solid">
                        <pre style="margin:0em">Hi,

I asked this question before.
Thanks to Justin, he did reply as follows.

Kiwoong Kim wrote:

    Hi,

    I'm getting better to use Gromacs owing to many posts on this sites :) .

    I have several questions about adding the counter-ions.


    My system has a number of N2 molecules which has charge,
    -0.40484(for single N) X 2.

    Thus, I have to add some counter-ions to make the system neutral.


    However, because I'm newbie on Gromacs, I thought of several
    clumsy ways myself.

    #1. Add virtual sites (virtual atoms) which has counter-ions like below.

    [ atomtypes ]
    ; name  mass   charge  ptype  sigma  epsilon
    DUM     0        0.80968 V    0.0    0.0


    I set the coordinates of each virtual DUM atoms to the center of
    N2 molecules.

    #2. using genion in Gromacs.


    But, I have no idea on this. What molecules do I have to designate
    to charge plus ion using genion ??

    I typed below line.

    genion -s md_0_1.tpr -n index.ndx -o ton_genion.pdb -g
    md_0_1_genion.log -p topol_genion.top -np 322 -pname dum -pq 0.80968

    and selected N2 molecules which is diffusing particle.


    It results that the name of half of N2 molecules is changed as
    DUM. (maybe the system become neutral)

    The number of N2 molecules should be fixed.

    Do I have additional N2 molecule for charging using genion?? Then,
    what are the initial coordinates???

    please help me....

    any advises would be helpful.

</pre>
                        <tt> How can I do that??? </tt><tt>I see no
                          reason why you should do either. For
                          dinitrogen, which has no </tt><tt>net dipole,
                          it seems intuitive to me that both N atoms
                          should have </tt><tt>zero charge.</tt>
                        <pre style="margin:0em">-Justin

I made linear rigid model (CO2) by introducing virtual interaction. However, I 
have troubles in modelling N2 molecules.
I want to model N2 with quadrupole moment according to the paper (Adsorption 
(2007) 13: 469-476).
In the paper, the charge N2 model (originally developed by Murthy et al. (1980) 
can be described as follows.
N (-0.40484), Dummy (N2, +0.80968).
</pre>
                      </blockquote>
                      <pre style="margin:0em">Right... that's totally different from N2 with charged N atoms :)

</pre>
                      <blockquote
style="margin:0em;padding-left:0.85em;border-left-color:rgb(85,85,238);border-left-width:0.2em;border-left-style:solid">
                        <pre style="margin:0em">Actually, I don't know how to model N2 molecules with dummy. Please let me know 
any advises.
</pre>
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                      <tt>Sounds like virtual site type 2 is perfect -
                        and didn't you already use </tt><tt>that for
                        CO2? See section 4.7 and somewhere in chapter 5.</tt>
                      <pre style="margin:0em">Mark

</pre>
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                        <pre style="margin:0em">Thx. Have a great day. :)


</pre>
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                    <pre style="margin:0em">&nbsp;</pre>
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