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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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