[gmx-users] using charmm36 force field with gromacs
jalemkul at vt.edu
Wed Nov 4 00:02:35 CET 2015
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 :)
> Kind regards,
> 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
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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
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