Potential Energy curve after the energy minimization

GROMACS version: 2020.2
GROMACS modification: No
System: C60 molecules inserted in a box

Hello everybody,

The energy minimization was completed successfully and the maximum force is less than 1000 kJ/mol/nm and the potential energy curve converges at the end, but the potential energy curve doesn’t look like the curve Justin showed in his online tutorials. Most of my y-axis is showing positive potential energy values while his curve shows only negative values.
I attached below a screenshot showing the difference between my curve (on the rights side) and Justin’s curve in the tutorial (on the left side).

Is that a problem and I need to continue energy minimization or it is fine as along ad the maximum force was less than 1000 and the energy converged at the end ?

If I still need to continue energy minimization, How can I do that ? should I decrease the maximum force value to be less than 1000 to make sure that the energy minimization will continue ?

Thanks,
Mohamed

I think your y-axis scale is too large to describe the minus region

1 Like

Thanks, I zoomed in and now I can see the y-axis are all with negative values.

You should not expect the results to be the same. They are different systems and have different forces. For a system of only C60 molecules, intermolecular interactions are weak and the total potential energy has a greater relative contribution from intramolecular (bonded) energy terms, which are strictly positive.

The tutorial system is a protein in water, which has many charged interactions (especially among water molecules) that dominate the total potential energy.

1 Like