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On 20/01/2012 5:51 PM, Kiwoong Kim wrote:
<blockquote
cite="mid:CALmcptAoT4tZbTQskVrAYCRy_KALk-ZYgMPnJQwCQmn87yYDKA@mail.gmail.com"
type="cite">Hi,
<div><br>
</div>
<div>I asked this question before. </div>
<div>Thanks to Justin, he did reply as follows. </div>
<div><br>
</div>
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<pre style="margin:0em">Kiwoong Kim wrote:
</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">Hi,
I'm getting better to use Gromacs owing to many posts on this sites :) .
I have several questions about adding the counter-ions.
</pre>
<tt>My system has a number of N2 molecules which has charge,
-0.40484(for </tt><tt>single N) X 2.</tt>
<pre style="margin:0em">Thus, I have to add some counter-ions to make the system neutral.
</pre>
<tt>However, because I'm newbie on Gromacs, I thought of
several clumsy ways </tt><tt>myself.</tt>
<pre style="margin:0em">#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
</pre>
<tt>I set the coordinates of each virtual DUM atoms to the
center of N2 </tt><tt>molecules.</tt>
<pre style="margin:0em">#2. using genion in Gromacs.
</pre>
<tt>But, I have no idea on this. What molecules do I have to
designate to </tt><tt>charge plus ion using genion ??</tt>
<pre style="margin:0em">I typed below line.
</pre>
<tt>genion -s md_0_1.tpr -n index.ndx -o ton_genion.pdb -g
md_0_1_genion.log </tt><tt>-p topol_genion.top -np 322
-pname dum -pq 0.80968</tt>
<pre style="margin:0em">and selected N2 molecules which is diffusing particle.
</pre>
<tt>It results that the name of half of N2 molecules is
changed as DUM. </tt><tt>(maybe the system become neutral)</tt>
<pre style="margin:0em">The number of N2 molecules should be fixed.
</pre>
<tt>Do I have additional N2 molecule for charging using
genion?? Then, what </tt><tt>are the initial coordinates???</tt>
<pre style="margin:0em">please help me....
any advises would be helpful.
</pre>
<tt>How can I do that??? </tt></blockquote>
<tt>I see no reason why you should do either. For dinitrogen,
which has no net </tt><tt>dipole, it seems intuitive to me
that both N atoms should have zero charge.</tt>
<pre style="margin:0em">-Justin
</pre>
<pre style="margin:0em"><span style="font-family:arial;white-space:normal">I made linear rigid model (CO2) by introducing virtual interaction. However, I have troubles in modelling N2 molecules.</span></pre>
<pre style="margin:0em"><span style="font-family:arial;white-space:normal">I want to model N2 with quadrupole moment according to the paper (Adsorption (2007) 13: 469-476).</span></pre>
<pre style="margin:0em"><span style="font-family:arial;white-space:normal">In the paper, the charge N2 model (originally developed by Murthy et al. (1980) can be described as follows.</span></pre>
<pre style="margin:0em"><span style="font-family:arial;white-space:normal">N (-0.40484), Dummy (N2, +0.80968).</span></pre>
</div>
</blockquote>
<br>
Right... that's totally different from N2 with charged N atoms :)<br>
<br>
<blockquote
cite="mid:CALmcptAoT4tZbTQskVrAYCRy_KALk-ZYgMPnJQwCQmn87yYDKA@mail.gmail.com"
type="cite">
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<pre style="margin:0em"><span style="font-family:arial;white-space:normal">
</span></pre>
<pre style="margin: 0em;"><font face="arial"><span style="white-space: normal;">Actually, I don't know how to model N2 molecules with dummy. Please let me know any advises.</span></font></pre>
</div>
</blockquote>
<br>
Sounds like virtual site type 2 is perfect - and didn't you already
use that for CO2? See section 4.7 and somewhere in chapter 5.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CALmcptAoT4tZbTQskVrAYCRy_KALk-ZYgMPnJQwCQmn87yYDKA@mail.gmail.com"
type="cite">
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<pre style="margin:0em"><font face="arial"><span style="white-space:normal"> </span></font></pre>
<pre style="margin:0em"><font face="arial"><span style="white-space:normal">
</span></font></pre>
<pre style="margin:0em"><font face="arial"><span style="white-space:normal">Thx. Have a great day. :)</span></font></pre>
<pre style="margin:0em">
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