[gmx-users] using charmm36 force field with gromacs

[Justin Lemkul]

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.

I suspect any errors would be rather small, but when it's easy to do things 
exactly right, that's the way to go :)

-Justin

> Kind regards,
> Erik
>
>
> lincs_iter    = 1                    ; accuracy of LINCS
> lincs_order    = 4                    ; also related to accuracy
> --
> ==================================================
>
> 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

==================================================