[gmx-users] Add counter-ions using virtual atom???
Justin A. Lemkul
jalemkul at vt.edu
Tue Jan 17 13:57:34 CET 2012
Kiwoong Kim wrote:
> 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
> #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
> #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 A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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