[gmx-users] Model N2 molecules

[Mark Abraham]

On 21/01/2012 12:04 AM, Kiwoong Kim wrote:
>
> Hi,
>

Please do keep the discussion on the list, so others can learn and 
contribute now and from the archives.

> I don't know how to model N2 molecule yet.
>
> If I use virtual site for N2 model, then, this can be done like below.
>
> Hence, where do I have to apply plus charge for making N2 neutral??
>
> Can it be D1 and D2 for plus charge??
>

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.

Mark

> Thx.
>
> [ atomtypes ]
>
> ; type mass charge ptype sigma epsilon
>
> D1 14.00674 0.0000 A 0.0000 0.00000000
>
> D2 14.00674 0.0000 A 0.0000 0.00000000
>
> N 0.0000000 -0.4048 V 0.332 0.3026
>
>   
>   [ moleculetype ]
>   ; name  nrexcl
>   N2         2
>   
>   [ atoms ]
>   ;   nr  type    resnr   residu  atom    cgnr    charge        mass
>   1       D1       1       N2    D1       1        0.0000  14.00674
>   2       D2       1       N2    D2       1        0.0000  14.00674
>   3       N        1       N2    N        1       -0.4048  0.0000000
>   4       N        1       N2    N        1       -0.4048  0.0000000
>   
> [ constraints ]
>   ;  ai  aj funct           c0           c1
>   1       2     1          0.1098
>   
>   [ virtualsites2]
>   ;  ai    aj    ak       funct   c0      c1
>        3     1     2       1       -0.5
>        4     1     2       1        0.5
>   
>   [ exclusions ]
> 3 4
> 4 3
> Below is the previous post message
> 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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