Hi,
I found the force field for Ni2+, Cd2+, and Zn2+ for the OPLS-AA, but I didn’t get it. Could anyone please tell me where I will get?
How can I add the nickel(2+) ions into the solution?
Will the below command work or not? ()
gmx genion -s ions.tpr -o file.gro -p topol.top -pname NI -neutral
Hi,
Just to avoid confusion Ni, Cd and Zn are not implemented by the with-GROMACS-distributed OPLS force field (as far as I recall). My guess you have implemented the corresponding parameters (generated in line with OPLS parameterization procedure) in the force field files. And include these files in the topology file.
gmx genion just modifies gro file by replacing water molecules with particles (representing ions) and change the topology file to account for these. If you want gmx genion has also options to specify the ion charge and concentration.
\Alessandra