[gmx-users] problem with system neutralization
smeliga at gmail.com
Fri May 22 11:50:23 CEST 2009
As the on-screen output of grompp says, my system has non-zero total
charge = -4.000
Thus, I'm trying to neutralize the system using genion with this command
genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p 4AKEallHsol_pre.top -neutral
The problem is that the on-screen output says:
"No ions to add and no potential to calculate"
as the system was already neutral, I guess.
I then tryied with the command line:
genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p 4AKEallHsol_pre.top
-neutral -np 50 -g
Ions are added to the SOL group but the total charge remains -4, as the
log file says.
Do you know the reason?
Thanks a lot,
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