<div>AFAIUI, when model CO2 molecules, at least two dummy particle should present to make CO2 linear-triatomic molecules along with the quadrupole moment. If there exists better way, I have to change CO2 model of mine. </div>
<div> </div><div>Thank you Mark and David :)<br><br></div><div class="gmail_quote">2012/1/20 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></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"><div class="im">
On 21/01/2012 12:40 AM, Kiwoong Kim wrote:
<blockquote type="cite">
<div>Hi, Mark.</div>
<div> </div>
<div>I'am very grateful to your reply.</div>
<div> </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 question under the disabled-subscribed
status. I haven't found the way to post the reply such status so
far. </div>
<div> </div>
<div>I will try to model N2 like you did mention. (two N atom
(Atom type: A), Dummy single N2 molecule (Atom type: V) between
N atoms) </div>
<div> </div>
<div>When I modeled CO2 (linear rigid body), I used below manner.
</div>
<div> </div>
<div> > [ atomtypes ]<br>
> ; type mass charge ptype c6
c12<br>
> D1 22.004975 0.0000 A
0.0000 0.00000000<br>
> D2 22.004975 0.0000 A
0.0000 0.00000000<br>
> C_CO 0.0000000 0.5406 V
0.0000 0.00000000<br>
> O_CO 0.0000000 -0.2703 V
0.29847 1.10765301<br>
> <br>
> [ moleculetype ]<br>
> ; name nrexcl<br>
> CO2 2<br>
> <br>
> [ atoms ]<br>
> ; nr type resnr residu atom cgnr
charge mass<br>
> 1 D1 1 CO2 DUM 1 0.0000
22.004975<br>
> 2 D2 1 CO2 DUM 1 0.0000
22.004975<br>
</div>
</blockquote>
<br></div>
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><span class="HOEnZb"><font color="#888888">
<br>
Mark</font></span><div><div class="h5"><br>
<br>
<blockquote type="cite">
<div>
> 3 C_CO 1 CO2 C_CO 1 0.5406
0.0000000<br>
> 4 O_CO 1 CO2 O_CO 1 -0.2703
0.0000000<br>
> 5 O_CO 1 CO2 O_CO 1 -0.2703
0.0000000<br>
> <br>
> [ constraints ]<br>
> ; ai aj funct c0 c1<br>
> 1 2 1 0.2006146447<br>
> <br>
> [ virtualsites2]<br>
> ; ai aj ak funct c0 c1<br>
> 3 1 2 1 0.4263443<br>
> 4 1 2 1 -0.07365569<br>
> 5 1 2 1 0.926344308<br>
> <br>
> [ exclusions ]<br>
> 4 3 5<br>
> 5 3 4<br>
> 3 5 4<br>
</div>
<div>Thanks Mark again. :)</div>
<div>
</div>
<div>Have a great day.<br>
</div>
<div class="gmail_quote">2012/1/20 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></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> </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><br>
<br>
<blockquote type="cite">
<div style="background:white"><span style="word-wrap:break-word" lang="EN-US">
<p> </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>’<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><font color="#888888"><br>
<br>
Mark</font></span>
<div>
<div><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> </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"></span> </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>
</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>
<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">Thx. Have a great day. :)
</pre>
</blockquote>
</span></div>
<div> </div>
<div> </div>
<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>
<div><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"></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"> </span></div>
<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"> </pre>
</blockquote>
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