[gmx-users] How to balance charge for modeling N2 molecules

Kiwoong Kim ilmarekw at gmail.com
Fri Jan 20 07:51:31 CET 2012


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

Kiwoong Kim wrote:


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

#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

#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.

How can I do that???

I see no reason why you should do either. For dinitrogen, which has no
net dipole,
it seems intuitive to me that both N atoms should have zero charge.


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).

Actually, I don't know how to model N2 molecules with dummy. Please
let me know any advises.

Thx. Have a great day. :)
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