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

[Mark Abraham]

On 20/01/2012 5:51 PM, Kiwoong Kim wrote:
> 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.
>
>     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.
> -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).

Right... that's totally different from N2 with charged N atoms :)

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

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.

Mark

>   
>
>
> Thx. Have a great day. :)
>
>

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