[gmx-users] Conversion between nonbonded charmm NBFIX and gromacs cross terms

[Justin Lemkul]

On 7/21/16 5:01 AM, Marlon Sidore wrote:
> Hello,
>
> I am currently translating non-bonded parameters from CHARMM to GROMACS,
> which include/necessitate cross terms for the forcefield I'm interested in
> (MARTINI).
>
> I am struggling at the conversion from the NBFIX lines, which have this
> shape:
> "P5 P5 -1.33843000 5.27557163
> P5 Nda -1.19503000 5.27557163"

So you're not dealing with CHARMM, but you're dealing with MARTINI parameters 
that happen to be in CHARMM format, correct?

> To something gromacs like, which have this shape:
> "  P5    P5  1   0.24145E-00     0.26027E-02 ; supra attractive
>   P5    Nda     1   0.21558E-00     0.23238E-02 ; attractive"
>
> I think I understood that CHARMM uses Rmin and Emin(epsilon) and GROMACS
> uses c6 and c12. But I'm currently stuck at how to translate the former

Force fields use whichever convention is specified in the [defaults] directive. 
The combination rule there can either specify the use of sigma/epsilon or C6/C12 
conventions.

CHARMM files specify epsilon and Rmin directly, so the conversions should be 
straigtforward:

epsilon (GMX) = epsilon (CHARMM) * 4.184 (and given as a positive value, by 
convention)

sigma (GMX) = Rmin (CHARMM) * 2^(-1/6) / 10

The values you have listed above have gone through the additional transformation 
of being converted to C6/C12 (after being converted to sigma/epsilon) by 
equation 5.1 in the manual for combination rule 1.

-Justin

> into the latter, as it doesn't seem like a simple scaling - since in this
> example 2 numbers from CHARMM are the same while none are the same in
> GROMACS.
>
> Thanks for your help
>
> Marlon Sidore
>
>
> PhD Student
> Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
> CNRS - UMR7255
> 31, Chemin Joseph Aiguier
> 13402 cedex 20 Marseille
> France
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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