[gmx-users] angle-angle and bond-angle cross terms

Justin Lemkul jalemkul at vt.edu
Wed May 28 01:07:20 CEST 2014

On 5/27/14, 10:34 AM, João T. S. Coimbra wrote:
> Dear All,
> I am fairly new to the GROMACS world.
> Recently I have came across 2 sections in the GROMACS manual intitled "angle-angle cross term" and "bond-angle cross term".
> I was wondering if it is possible to implement these additional parameters for the commonly available force fields: AMBER, GROMACS and CHARMM (in regards to protein simulations).
> I have tested the Morse potential with the AMBER ff99SB, and this only needs a keyword for selecting this potential. For the case of bond-angle and angle-angle cross terms I cannot find such "keyword-modes". Does this mean that a carefull parameterization of such cross terms is needed?
> If so, can I then implement such MM terms in the previously discussed force fields?

Sure, but doing so would likely require a massive reparametrization of any of 
those force fields.  It's not trivial to simply add in a new term to the 
functional form; everything is balanced against existing terms.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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