[gmx-users] genion

[Ewaru]

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:

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,



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