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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