[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:
> 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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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