[gmx-users] using charmm36 force field with gromacs

[Mark Abraham]

Hi,

Pages are back at
http://www.gromacs.org/Documentation/Terminology/Force_Fields

Mark

On Wed, Nov 4, 2015 at 1:14 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/4/15 4:52 AM, Catarina A. Carvalheda dos Santos wrote:
> > Hi Justin,
> >
> > Regarding the nonbonded settings for protein-membrane simulations using
> > CHARMM.
> > The information you provided used to be available at http://www.
> > <
> http://www.google.com/url?q=http%3A%2F%2Fwww.gromacs.org%2FDocumentation%2FTerminology%2FForce_Fields%2FCHARMM%3Fhighlight%3Dcharmm&sa=D&sntz=1&usg=AFQjCNExpa_o_HvFT4jyZ4M99zVk-TyRwQ
> >
> > gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
> > <
> http://www.google.com/url?q=http%3A%2F%2Fwww.gromacs.org%2FDocumentation%2FTerminology%2FForce_Fields%2FCHARMM%3Fhighlight%3Dcharmm&sa=D&sntz=1&usg=AFQjCNExpa_o_HvFT4jyZ4M99zVk-TyRwQ
> >,
> > but I do not seem to be able to find it now (even using the search
> engine).
> >
> > I know the GROMACS website has gone through some changes lately, so maybe
> > this was just moved somewhere else.
> > Could you please tell us where we can find it now?
> >
>
> The page was deleted during a recent wiki cleanup/purge.  I hope it will be
> reinstated, along with some of the other useful force field pages that we
> had.
>
> -Justin
>
> > Kind regards,
> >
> >
> > On 4 November 2015 at 08:43, Erik Marklund <erik.marklund at chem.ox.ac.uk>
> > wrote:
> >
> >>
> >> On 3 Nov 2015, at 23:51, Justin Lemkul <jalemkul at vt.edu<mailto:
> >> jalemkul at vt.edu>> wrote:
> >>
> >>
> >>
> >> On 11/3/15 6:45 PM, Erik Marklund wrote:
> >>
> >> On 3 Nov 2015, at 23:02, Justin Lemkul <jalemkul at vt.edu<mailto:
> >> jalemkul at vt.edu><mailto:jalemkul at vt.edu>> wrote:
> >>
> >>
> >>
> >> On 11/3/15 5:53 PM, Erik Marklund wrote:
> >>
> >>
> >>
> >>
> >> Use constraints = h-bonds
> >>
> >> You'll get incorrect balance of 1-4 interactions if you constrain all
> >> bonds with CHARMM.
> >>
> >> Interesting. Can you please elaborate Justin?
> >>
> >>
> >> Think about a simple C-C-C-C dihedral.  In our CHARMM parametrization,
> we
> >> assume all of those bonds to be harmonic and tune the dihedral energy
> >> surface against QM target data that have only one constraint - the
> dihedral
> >> itself.  Therefore, the bond lengths can vary, and since the dihedral
> term
> >> and the 1-4 nonbonded terms are interrelated (and everything else is
> >> excluded), the balance of forces depends on the correct application of
> the
> >> bonded terms.  So to use the force field in the same manner as it was
> >> parametrized, constrain only bonds involving H.
> >>
> >>
> >> Thanks. I do get that. But is charmm any different from other widely
> used
> >> protein force field in this respect?
> >>
> >>
> >> Not that I'm aware.  Again, given the magnitude of the fluctuations of
> >> bonds, the magnitude of any error would probably be extremely small so I
> >> would not expect serious problems if one were to constrain all bonds.
> Just
> >> pointing this out for the sake of being pedantic, but it is something I
> >> think should be done properly, since the functional form assumes it in
> the
> >> parametrization.
> >>
> >> -Justin
> >>
> >> Right. Thanks for clarifying Justin.
> >>
> >> Erik
> >>
> >>
> >> --
> >> ==================================================
> >>
> >> 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<mailto:
> jalemkul at outerbanks.umaryland.edu>
> >> | (410) 706-7441
> >> http://mackerell.umaryland.edu/~jalemkul
> >>
> >> ==================================================
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> >
> >
> >
>
> --
> ==================================================
>
> 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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