[gmx-users] Lennard Jones parameters for Sp, Sp2 and Sp3 nitrogen identical?

[Justin Lemkul]

On 10/22/15 11:04 AM, Ebert Maximilian wrote:
> Dear list,
>
> I already asked the question in the AMBER list but couldn’t get an answer. So I try my luck here even though it is a bit off topic in the GROMACS list. I was wondering why the different atom types of H, C and O have different LJ-parameter but for all the different types of N we see the identical parameters in OPLS, AMBER and CHARMM?
>

Sometimes that's just the way force fields work out.  Electrostatics are tuned 
first, and then condensed phase interactions are targeted for LJ refinement. 
Given the nature of most N interactions (either lone pair or via polar/hydrogen 
bonding interactions with an H), the electrostatics generally dominate, so a 
generic LJ parameter that is common to different moieties is sufficient.

In CGenFF, there are several N types with different LJ, though the biomolecular 
parts of the CHARMM force field share the same parameters.

-Justin

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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

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