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    On 21/01/2012 12:04 AM, Kiwoong Kim wrote:
    <blockquote
cite="mid:CALmcptBCJ2XYNXEw-VjFF3wcqrwB9ADbuOkfrmgyNqyNnNtRzA@mail.gmail.com"
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          <p><span lang="EN-US"> Hi,</span></p>
          <p><span lang="EN-US"></span></p>
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    </blockquote>
    <br>
    Please do keep the discussion on the list, so others can learn and
    contribute now and from the archives.<br>
    <br>
    <blockquote
cite="mid:CALmcptBCJ2XYNXEw-VjFF3wcqrwB9ADbuOkfrmgyNqyNnNtRzA@mail.gmail.com"
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          <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>
    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.<br>
    <br>
    Mark<br>
    <br>
    <blockquote
cite="mid:CALmcptBCJ2XYNXEw-VjFF3wcqrwB9ADbuOkfrmgyNqyNnNtRzA@mail.gmail.com"
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          <p
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            <span lang="EN-US"> </span></p>
          <p
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            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"
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            <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"
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            <span lang="EN-US">; type mass charge ptype sigma epsilon</span></p>
          <p
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            <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>
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      <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>
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          <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>
          </blockquote>
          <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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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">Thx. Have a great day. :)


</pre>
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