Define net charge on molecule while using QEq

You shouldn’t use the following:

fix qeq1 Ni qeq/dynamic 1 10 1.0e-3 200 param.qeq1

fix qeq2 MOF qeq/dynamic 1 10 1.0e-3 200 param.qeq1

fix qeq3 water qeq/dynamic 1 10 1.0e-3 200 param.qeq1

You should use this:

fix qeq1 all qeq/dynamic 1 10 1.0e-3 200 param.qeq1

With QEq, you don’t assign charges to atoms but the QEq algorithm does, so you don’t need to worry about “but I don’t know how to assign charge for it.” The only freedom you have with fix qeq/dynamic is the system charge, which you have set to +2 by assigning +2 to 1 Ni atom, but this +2 is redistributed to the entire system and does not stay on the Ni atom.

You are doing three things wrong:

Typo correction:

  1. When I used your “incorrect” qeq parameters on pure water (single point energy) I got q_H = 0.054. When I used correct parameters q_H = 0.25.

Ray