[gmx-users] Adapting metallic ions from AMBER to GROMACS

[Mark Abraham]

Hi,

Convert the units and absorb the factor of two to the minus six. Compare
with other ions present in both representations of such force fields.

Mark

On Tue, 19 Apr 2016 02:21 Pedro Lacerda <pslacerda+gmx at gmail.com> wrote:

> Hi Gromacs users,
>
> We are planning a simulation with a metallic (fe+2) attached on the
> protein. The parameters found in [1] cannot be directly inserted on
> ffnonbonded.itp because equation 1 of [1] and equation 4.5 of [2] are
> slightly different.
>
> Theoreticaly these Lennard-Jones parameters could be used in any PME based
> force field, but it was derived and tested using the AMBER software and
> potential, so it is our current force field of choice. In
> amber99sb-ildn/ffnonbonded.itp the long range interactions are described in
> terms of epsilon (kJ/mol) and sigma (Rmin; nm).
>
> Eq 1:
>
>     Lj = 4e ((R/r)^12 - (R/r)^6)
>
> Eq 4.5:
>
>     Lj = e ((R/r)^12 - 2(R/r)^6)
>
> Seems that Rmin values are written as Rmin/2 in AMBER files avoiding some
> calculations to optimize the software. But this occurs at implementation
> level and probably does not have correspondence with the paper.
>
> My question is how can I adapt these parameters so they can be used in
> Gromacs?
>
> (Sorry about the previous email, now the title is correct)
>
> [1]
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3728907/pdf/nihms481931.pdf
>
> [2] ftp://ftp.gromacs.org/pub/manual/manual-5.1.2.pdf
>
> [3] http://comments.gmane.org/gmane.science.biology.gromacs.user/82242
>
>
> Cheers,
>
> Pedro Lacerda
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