[gmx-users] Model N2 molecules

Kiwoong Kim ilmarekw at gmail.com
Fri Jan 20 14:40:23 CET 2012


Hi, Mark.

I'am very grateful to your reply.

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.

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)

When I modeled CO2 (linear rigid body), I used below manner.

 > [ atomtypes ]
> ;   type      mass    charge    ptype       c6            c12
>     D1         22.004975        0.0000       A         0.0000
0.00000000
>     D2          22.004975       0.0000       A         0.0000
0.00000000
>     C_CO     0.0000000          0.5406       V         0.0000
0.00000000
>     O_CO     0.0000000         -0.2703       V         0.29847
1.10765301
>
> [ moleculetype ]
> ; name  nrexcl
> CO2         2
>
> [ atoms ]
> ;   nr  type    resnr   residu  atom    cgnr    charge        mass
> 1       D1       1       CO2    DUM       1        0.0000  22.004975
> 2       D2       1       CO2    DUM       1        0.0000  22.004975
> 3       C_CO     1       CO2    C_CO      1        0.5406  0.0000000
> 4       O_CO     1       CO2    O_CO      1       -0.2703  0.0000000
> 5       O_CO     1       CO2    O_CO      1       -0.2703  0.0000000
>
> [ constraints ]
> ;  ai  aj funct           c0           c1
> 1       2     1          0.2006146447
>
> [ virtualsites2]
> ;  ai    aj    ak       funct   c0      c1
>      3     1     2       1       0.4263443
>      4     1     2       1      -0.07365569
>      5     1     2       1       0.926344308
>
> [ exclusions ]
> 4 3 5
> 5 3 4
> 3 5 4
Thanks Mark again. :)

Have a great day.
2012/1/20 Mark Abraham <Mark.Abraham at anu.edu.au>

>  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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>
>
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