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

Pedro Deira pedro.deira at gmail.com
Mon Jan 15 15:57:41 CET 2018

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 ?

- 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?

Thanks for any comments,
All the best,

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