[gmx-users] GROMOS force field for small molecules

[Justin Lemkul]

On 7/11/19 10:19 AM, Edjan Silva wrote:
> Dear users,
>
> Is the use of the GROMOS force field for small molecules reliable?
> I performed complex DNA-LIG simulations and noticed slight distortions in
> the binding angles of some functional groups such as the −C
> <https://en.wikipedia.org/wiki/Carbon>≡N
> <https://en.wikipedia.org/wiki/Nitrogen>  functional group.
> Can these distortions be related to some error in the standardization of
> the types of atoms, or is it just the inability of the force field to
> simulate small molecules?

The quality of the topology dictates the quality of the results. Any 
force field can be made to model anything properly, with sufficient 
effort. I've never seen anyone use GROMOS for nucleic acids; CHARMM and 
AMBER are the standards for those types of simulations and parametrizing 
small molecules for those force fields is largely automated (and 
straightforward to refine).

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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