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, -- 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. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
