[gmx-users] Inconsistent non-bonded energy when using energy tables.

[Mark Abraham]

Hi,

Whether you will have a reasonable way to have your nonbonded interaction
parameters combine with combination rules is up to you to decide, but AFAIK
this should work. You will have a much better time trouble shooting your
setup if you use
http://manual.gromacs.org/documentation/current/user-guide/mdrun-features.html#re-running-a-simulation
rather
than some contrived simulation to evaluate potential energies.

Mark

On Wed, May 2, 2018 at 1:27 PM Samuel Ntim <samuel.ntim at live.co.uk> wrote:

> Dear All,
>
> I will be working with a system having Lennard-Jones interactions between
> some species and Buckingham interactions between other species. I know this
> is possible using tables.
>
> As a first check to be sure I am doing the right thing, I set up a minimal
> system of two particles fixed in their initial positions and without
> charges. When I run a short simulation on this system with and without
> tables, I get similar non-bonded energy contributions to the total energy.
>
> However, when I increase the number of particles to three, each
> equidistant from the the other two, I get a different contribution with
> tables, from without tables. Without tables, I get about three times the
> contribution in the previous set up (which is what I expect), but with
> tables the energy is only slightly different from that of the two-particle
> system.
>
> I have attached the two simple systems and the files used in running the
> simulations in a .rar file here<
> https://www.dropbox.com/s/v9x7zb0tu4mkn5p/SIMPLE.rar?dl=0>.
>
> I will be glad to have someone point me in the right direction. Thank you.
>
>
> Best regards,
> Samuel
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