[gmx-users] Multisite ion of Mg in Gromacs

[Quyen Vu]

Dear all,
Could anyone can please help me clarify the last paragraph on page 393 of
gromacs manual 2019.1?

"when sigma and epsilon need to be supplied (rule 2 and 3), it would seem
it is impossible to have non-zero C12 combined with a zero C6 parameter.
However, providing a negative sigma will do exactly that, such that C6 is
set to zero and C12 is calculated normally"

If the reference uses the potential function: U_{ij}=Aij/r_{ij}^12
-B_{ij}/r_{ij}^6 and provide A_i=0.05, B_i=0, how can I convert to epsilon
and sigma in Gromacs (using amber99sb force field)?
Thank you and best regards,


On Fri, May 24, 2019 at 12:15 PM Quyen Vu <vuqv.phys at gmail.com> wrote:

> Dear GMX users,
> I want to use multisite ion model for Mg2+ and I follow the parameters set
> of the paper: https://pubs.acs.org/doi/10.1021/jp501737x
> Here they develop these parameters for Q package. In the Lennard-Jones
> potentials, they use Aij, Bij terms (eq. 1) while Gromacs use epsilon and
> sigma term. The dummy atoms in their model have the repulsive term (Ai) but
> not attractive term (Bi=0).
>  How can I remove the attractive term of dummy atoms in Gromacs?
> Best regards,
> Quyen
>