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 <[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. :) > > > > > > > > > > > > > > > > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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