[gmx-users] using charmm36 force field with gromacs

[Catarina A. Carvalheda dos Santos]

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?

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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-- 
Catarina A. Carvalheda

PhD Student
Computational Biology Division
School of Life Sciences
University of Dundee
DD1 5EH, Dundee, Scotland, UK