[gmx-users] genion

[Justin Lemkul]

On 5/3/13 11:27 AM, Ewaru wrote:
> Hi,
>
> Just wondering. My system shows this: "System has non-zero total charge:
> 11.999998"
> and thus, I use the command as below to add 12 Cl to the protein:
>
> "genion -s ions.tpr -o m4_solv_ions.gro -p topol.top -pname NA -nname CL -nn
> 12"
>
> However, when I checked the genion.log file, it shows that the system has
> total charge of 12. Isn't it supposed to be 0? This is what the genion.log
> shows:
>

The charge that genion reports is the one that it finds in the system contained 
in the .tpr file.  grompp reports a net charge of 12 (or close enough to it, see 
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic) and genion 
confirms that is what it finds.  The next invocation of grompp will confirm that 
your net charge is zero.

-Justin

> Will do ordinary reciprocal space Ewald sum.
> Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
> Using shifted Lennard-Jones, switch between 0 and 1 nm
> Cut-off's:   NS: 1   Coulomb: 1   LJ: 1
> System total charge: 12.000
> Generated table with 1200 data points for Ewald.
> Tabscale = 500 points/nm
> Generated table with 1200 data points for LJ6Shift.
> Tabscale = 500 points/nm
> Generated table with 1200 data points for LJ12Shift.
> Tabscale = 500 points/nm
> Generated table with 1200 data points for 1-4 COUL.
> Tabscale = 500 points/nm
> Generated table with 1200 data points for 1-4 LJ6.
> Tabscale = 500 points/nm
> Generated table with 1200 data points for 1-4 LJ12.
> Tabscale = 500 points/nm
>
> Enabling SPC-like water optimization for 3745014 molecules.
>
> Thank you.
>
> Best regards,
>
>
>
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/genion-tp5007916.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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