[gmx-users] Calculation of an energy term for stretching

[Alessandra Villa]

Hi,

Below some suggestions
On Thu, Jan 23, 2020 at 3:52 PM <nikolaev at spbau.ru> wrote:

> Dear collegues,
>
> I am trying to write an energy function for my molecule that will imitate
> the results of the amber energy function. For this reason, I calculated
> all energy terms for my molecule (printed all terms for the 0-th step in
> energy minimization).
> However, I find a problem in the very first formula: a harmonic potential
> for bond stretching. I get the results twice as large as gromacs.
> I use amber potential. The force constants are of magnitude ~250 000.0
> I apply the formula k/2 (b - b0)^2. Amber99 force field.
> Where can the problem come from?
>
>
Maybe a bad unit conversion while you convert the dimension to GROMACS unit
(see
http://manual.gromacs.org/documentation/2019-current/reference-manual/definitions.html?highlight=gromacs%20unit
)
Maybe a difference in the analytical formula in GROMACS for the
potentialthe one use in AMBER  ( e.i k vs k/2 )
For interaction potential formula see
http://manual.gromacs.org/documentation/2019-current/reference-manual/functions.html
For the potential format see Table 14 in

http://manual.gromacs.org/documentation/2019-current/reference-manual/topologies/topology-file-formats.html?highlight=table%20force%20field
Best regards
Alessandra



> My molecular system is a molecule of 57 atoms, in vacuum.
>
> Best,
> Dmitrii
>
>
>
>
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