[gmx-users] Conversion of charmm36 parameters from namd to gromacs

[Justin Lemkul]

On 12/4/17 12:21 PM, Daniel Bauer wrote:
> Hello,
>
> I finally found my error in the conversion. As always, the devil is in
> the detail. I was under the assumption that parameters listed in the
> original forcefield files (toppar) are also sigma and epsilon values.
> However, as you know, the original files list Rmin values (and not sigma).
>
> With the correct conversion term:
>
> eps = Rmin/(10*2^(1/6))
>
> I can now reproduce the conversion of the numbers from the charmm
> implementation to gromacs (and thus know how to apply my NBFIX for this
> value).

I don't know what NBFIX you might have, but FYI there is a value that 
will become official in the next release of the force field. We've 
validated it against proteins and nucleic acids. See the SI of 
http://dx.doi.org/10.1128/AAC.01572-17

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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