[gmx-users] Add counter-ions using virtual atom???

Kiwoong Kim ilmarekw at gmail.com
Tue Jan 17 12:04:56 CET 2012


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???
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