[gmx-users] Fwd: two very basic questions on new parameters for gromos forcefield

[Justin Lemkul]

On 1/15/18 9:57 AM, Pedro Deira wrote:
> Dear all,
>
> I have been working with some new molecules and some new bonded parameteres
> that I added to the gromos 54a7 files in gromacs according to the manual
> and so on, and all the results of MD simulations are in perfect agreement
> with the experimental results.
>
> However, I've just been reviewing this odd paper and I'm stuck with these
> very very basic questions that make me question if I'm working as I should:
>
> - When we select a gromos force field, or derivative, it will use, for
> example, the force constants provided in the definition files for that ff,
> and those are written in agreement with table 5.5 of the manual, say, bond
> force constant comes in kJ mol-1 nm-4, right ?

Yes.

> - Therefore, when we compute the force constant values, we should use the
> equation from the corresponding force field, right? For example, for
> gromos96 fourth power potential (page 74 of 2018 manual), the value we
> include in the ff parameters if the k_ij^b in equation 4.35, and not any
> other value, right?

Yes.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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