[gmx-users] Model N2 molecules
Kiwoong Kim
ilmarekw at gmail.com
Fri Jan 20 14:40:23 CET 2012
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
> 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. :)
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120120/18912b1d/attachment.html>
More information about the gromacs.org_gmx-users
mailing list