[gmx-users] problem with genion

[Justin A. Lemkul]

sarbani chattopadhyay wrote:
>  
> 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.
>

Probably your box size is such that 0.00001 is interpreted as zero.  Gromacs 
calculates concentrations by taking the volume of the unit cell in the .tpr 
file, and it probably rounds 10 uM to zero.

-Justin


> However I can't figure out what is the problem with the low 
> concentration command.
> 
> Any suggestion will be extremely heplful.
> Thanks in advance
> Sarbani
> 
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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