Potential Energy curve after the energy minimization

User discussions
1

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).

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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

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

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

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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.

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5

Hi

I’m also experiencing the same issue with a positive potential energy even if max force was < 1000. Is it possible to carry on with equilibration?
Please let me know the solution to resolve it?
If more minimisation is needed please let me know the command to continue minimisation from previous step. Thank you.