[gmx-users] Model N2 molecules

Kiwoong Kim ilmarekw at gmail.com
Fri Jan 20 14:04:19 CET 2012


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??


[ 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:


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 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.


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.


Thx. Have a great day. :)
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120120/d10eae1e/attachment.html>

More information about the gromacs.org_gmx-users mailing list