[gmx-users] problem with genion

sarbani chattopadhyay sarbani_c84 at rediffmail.com
Wed Sep 24 08:46:56 CEST 2008

Hi everyone,
                  I am facing a peculiar problem with "genion". I have a system with overall charge 
0f +3. 
I want genion to add enough ions to make the cocncentration 10 micromoles/litre.
When I give the command 
genion -s em.tpr -o ions.gro -conc 0.00001 -pname NA+ -nname CL- -p topol.top ,

it gives the message
"No ions to add and no potential to calculate."
If I use the "-neutral" option with the "genion " command, it adds 3 CL- ions.

However it works perfectly fine when I specify the concentration to be 0.15 Moles/litre.
The number of ions added to the system matches with calculations done manually.

However I can't figure out what is the problem with the low concentration command.

Any suggestion will be extremely heplful.
Thanks in advance
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