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

[Kroon, P.C.]

As an aside: Martini forcefield parameters are available in Gromacs format
on the Martini website. See
http://cgmartini.nl/index.php/force-field-parameters

Peter

On Thu, Jul 21, 2016 at 2:05 PM, Marlon Sidore <marlon.sidore at gmail.com>
wrote:

> Thanks for your answer, that solved everything.
>
> Marlon
>
> Marlon Sidore
>
>
> PhD Student
> Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
> CNRS - UMR7255
> 31, Chemin Joseph Aiguier
> 13402 cedex 20 Marseille
> France
>
>
> 2016-07-21 14:01 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
>
> >
> >
> > 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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