On 2012-01-20 14:04, Kiwoong Kim wrote:
Hi,
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??
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
What is the physical meaning of a N2 molecule with net charge -0.8 ?
For a physical model with three particles I would suggest to make the
atoms +0.1 or so and the central virtual particle -0.2. This is
realistic since the triple bond between the atoms yields a significant
electron density. In order to tune the charges you should compute the
quadrupole moment and compare that to high level AI calculations or
experimental data.
You might want to check this reference for a more complex N2 model:
Jordan et al. J. Chem. Phys. 103 (1995) p. 2272-2285.
[ 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. :)
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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