[gmx-users] Model N2 molecules
Kiwoong Kim
ilmarekw at gmail.com
Fri Jan 20 15:21:45 CET 2012
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 :)
2012/1/20 Mark Abraham <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>
>
>> 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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