Positive potential and wrong pressure after NPT! What’s the problem?

User discussions
1

GROMACS version: 2018
GROMACS modification: Yes/No
I use gromacs to simulate asphaltene molecules (poly aromatic molecules exist in oil) and study their aggregation behavior.I use OPLS/aa ff and I have nearly 103000 atoms which is belong to asphaltene, heptane and toluene molecules (cubic simulation box, 12 12 12).
my procedure is : optimize molecules with gaussian 09 > build simulation box > EM > NVT > NPT
after NPT for 3 ns, two things happened that I have to concern: first, there is a problem with pressure! it’s about -1.1 bar (which I set 1 bar). second problem is potential. It’s in the currect order of e05 but it’s positive! according to the literature, it must be negative.
worth mentioning that after EM everything seems all right (potential is negative and Fmax< emtol). I don’t understand what’s wrong.

thanks in advance.
nasrola

2

This is not a problem. See http://manual.gromacs.org/current/user-guide/terminology.html#fluctuation

What literature tells you the potential energy of your system? Are you reproducing a previously simulated system?

Your molecules are only going to have weak nonbonded interactions, therefore the potential energy of the system is dominated by bonded interactions, which are strictly positive. Negative potential energy is only expected in condensed-phase systems like biomolecules in water, because the potential energy is dominated by favorable electrostatic interactions in the solvent.

3

thanks @jalemkul for your answer
yes, I do the same but with different ff. It’s just a start. I will use two new inhibitor to prevent aggregation of asphaltenes in further simulations. for now, I want to validate my system with literature.
Actually I’m so confused now because base on the paper, I have to get negative potential. I also have their supplementary. please help me to understand where the problem is.
best regard

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You won’t get the same outcome if you’re using a different force field. The total potential energy of the system is a force field-dependent, and ultimately physically meaningless, quantity.

5

I see terminology and check my result again, my pressure fluctuate between ±150 bar with average pressure of -1.1 bar. For assurance I ask, are they normal?
again, thanks for your time.

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So in your opinion, my system is working well and I can do the production run, right?

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I’m not able to say anything definitively because I do not know any details about your force field parametrization and validation, but (1) positive potential energy is possible and is not necessarily a sign of problems and (2) your pressure is normal.