[gmx-users] control parameter on the Lennard-Jones interactions

[Omkar Singh]

I have protein MD simulation file I want to find out protein water rdf with
coordination number. Can anyone help regarding this?

Thanks


On Thu, May 16, 2019, 10:55 <battistia at libero.it> wrote:

>
> Dear gromacs members,
>
> I would ask you if in gromacs is possible to add a control parameter on
> the Lennard-Jones interactions.
> For example we have two atoms A and B and the corresponding parameters;
> sigma(A), eps(A),  sigma(B), esp(B); then for the A-B interactions we have
> the parameters obtained with the Lorentz-Berthelot or with the geometrical
> average.
>
> I would like to have a standard interaction between A or B with the other
> atoms of the system.  In the same time I would like to add a control
> parameter C on the interaction between A and B to have the following
> potential:
> V(r(AB))=4*eps(AB)*[(sigma(AB)/r(AB))^(12)-C*(sigma(AB)/r(AB))^(6)]
>
> Is it possible? How can I manage this calculation?
>
>
> Many thanks,
>
>
> Anna
>
>
>
>
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