[gmx-users] using charmm36 force field with gromacs

[Erik Marklund]

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


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

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