GROMACS modification: Yes/No
I want to calculate the interaction energy between the two species. But every time I calculate the same simulation, the interaction energy varies between 250 and 600. I use the NVT ensemble. There is a vacuum inside the simulation box, and I use 148 core CPU.
gmx mdrun -v -deffnm nvt -nb cpu -pme cpu -pmefft cpu -bonded cpu -update cpu -pin auto -tunepme yes -reseed 123456789 -dlb yes
Before I answer I would like to say that your behavior is very unpolite. GROMACS is not a commercial software that you can demand support for, but free open-source software and many of the people answering questions on this forum are doing that to be helpful and are not begin paid for answering.
The answer to your question is that molecular dynamics is chaotic and mdrun is not binary reproducible (unless you use the -reprod flag and even then runs sometimes are not reproducible). So trajectories, also starting from the same tpr file, diverge exponentially in time.
I have a question: Are you re-running both nvt and interaction.tpr each time? If you repeat just the second part (interaction.tpr) on a single nvt run do you get consistent result? In other words, at which stage is the inconsistency creeping in?
Thank you very much, Hess. I did not mention you intentionally. I just saw that you answered a few questions a few hours ago, and I thought you could help solve this problem. Because I posted this question a long time ago, and no one answered. I apologize for my behavior that upset you.
I had a question about the -reprod flag. Does the interaction energy change decrease when I use this flag? The interaction energy I calculated is a variable range of 250-600. Does this change range decrease?
So if you just rerun the second calculation you get the same results, right?
That tells you that your nvt runs are not identical. Have you looked at your coordinates at the ends of the nvt runs? Are they identical? I would guess not.
This could be because of numerical instabilities or because of different random seeds. See hess’s answer above for a more precise answer.