On 21/01/2012 12:40 AM, Kiwoong Kim wrote:
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
Here the two dummy atoms are used to give the rigid CO2 the moments of
inertia of a diatomic molecule. Whether that's reasonable would have to
be seen in the results there...
Mark
> 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 <[email protected]
<mailto:[email protected]>>
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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