[gmx-users] Coulomb 1-4 interactions

[Mark Abraham]

> Hi gmx-users:
>
> I am running a comparison between AMBER and Gromacs for a AOT system.
> First
> I created the AMBER force field and then transformed it to Gromacs force
> field.

There are existing ports that you can find in the User Contributions
section of the GROMACS webpage. Comparing yours with theirs may well be
instructive for somebody.

> I did 1 step of MD respectively in AMBER and Gromacs with the same
> configuration. All the energy terms including bond, angle, dihedral, LJ
> (SR), LJ (14) and Coulomb (SR) are the same with each other between the
> two
> runs except the Coulomb (14) interaction. What might be the reason for
> this?

Various force fields routinely scale this interaction. Check the papers
that describe the implementation of the AMBER force field for information
here. Then read the GROMACS manual to work out how to implement the same.

> I have totally no idea. Because the LJ (14) and Coulomb (14) calculation
> use
> the same 1-4 pairs in Gromacs, the LJ (14) is the same which means the 1-4
> pairs are the same between AMBER and Gromacs. The Coulomb (SR) is the same
> which means the charges are the same between AMBER and Gromacs. (I also
> checked these two things explicitly between AMBER and Gromacs.) How could
> the Coulomb (14) be different then? Does any one have any idea about how
> the
> coulomb (14) interactions are calculated in AMBER and Gromacs? Thanks a
> lot.

See above - read the original papers.

Mark