[gmx-users] Model N2 molecules
David van der Spoel
spoel at xray.bmc.uu.se
Fri Jan 20 15:57:08 CET 2012
On 2012-01-20 15:21, Kiwoong Kim wrote:
> AFAIUI, when model CO2 molecules, at least two dummy particle should
> present to make CO2 linear-triatomic molecules along with the quadrupole
> moment. If there exists better way, I have to change CO2 model of mine.
> Thank you Mark and David :)
Working on it, but not yet finished.
>
> 2012/1/20 Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>>
>
> 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 <Mark.Abraham at anu.edu.au
>> <mailto: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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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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