[gmx-users] Model N2 molecules
Mark Abraham
Mark.Abraham at anu.edu.au
Fri Jan 20 14:19:18 CET 2012
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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