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 <[email protected]> > 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 <[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 >> > > > > > > -- > 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 >
-- 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
