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

[Marlon Sidore]

Thanks.
It was actually more to try to see why our simulations have been crashing
on NAMD when using Martini, while the systems I built using insane and ran
only on gromacs went smoothly.

And I still don't know why to be honest, since the simulation (now
converted from NAMD to gromacs) actually doesn't seem to crash at all on
gromacs.

Marlon Sidore


PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
France


2016-07-22 16:27 GMT+02:00 Kroon, P.C. <p.c.kroon at rug.nl>:

> 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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