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

[nikolaev at spbau.ru]

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?

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

Best,
Dmitrii