# Why is it different every time the interaction energy is calculated? **URL:** \ **Category:** User discussions\ **Tags:** mdp-parameters, mdrun\ **Created:** [April 5, 2022, 7:54am UTC](https://gromacs.bioexcel.eu/t/why-is-it-different-every-time-the-interaction-energy-is-calculated/3956 "2022-04-05T07:54:13Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![Reza](https://avatars.discourse-cdn.com/v4/letter/r/b4bc9f/32.png) [@Reza](https://gromacs.bioexcel.eu/u/Reza)\ **Post date:** [April 5, 2022, 7:54am UTC](https://gromacs.bioexcel.eu/t/why-is-it-different-every-time-the-interaction-energy-is-calculated/3956/1 "2022-04-05T07:54:13Z")
GROMACS version:2021 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. forcefield=charmm36 gmx mdrun -v -deffnm nvt -nb cpu -pme cpu -pmefft cpu -bonded cpu -update cpu -pin auto -tunepme yes -reseed 123456789 -dlb yes gmx grompp -f Interaction\_energy.mdp -c nvt.gro -p topol.top -o Interaction.tpr gmx mdrun -s Interaction.tpr -rerun nvt.xtc -nt 1 gmx energy -f ener.edr -o Interactionenergy.xvg \> Interaction.log **nvt.mdp** integrator = md-vv nsteps = 10000000 dt = 0.001 nstlist = 10 rlist = 1.4 cutoff-scheme = Verlet vdw-type = PME rvdw = 1.4 coulombtype = P3M-AD DispCorr = Ener lj-pme-comb-rule = Lorentz-Berthelot rcoulomb = 1.4 tcoupl = v-rescale tc-grps = system tau-t = 0.1 ref-t = 353 pbc = xyz gen-vel = yes gen-temp = 353 gen-seed = 123456789 ld-seed = 123456789 constraints = none freezegrps = \*\*\*\* freezedim = Y Y Y Y Y Y nstxtcout = 10000 nstxout = 10000 nstenergy = 10000 **Interaction\_energy.mdp** integrator = md-vv nsteps = 10000000 dt = 0.001 nstlist = 10 rlist = 1.4 cutoff-scheme = Verlet vdw-type = PME rvdw = 1.4 coulombtype = P3M-AD DispCorr = Ener lj-pme-comb-rule = Lorentz-Berthelot rcoulomb = 1.4 tcoupl = v-rescale tc-grps = system tau-t = 0.1 ref-t = 353 pbc = xyz gen-vel = yes gen-seed = 123456789 ld-seed = 123456789 gen-temp = 353 constraints = none energygrps = \*\* \*\* nstxtcout = 10000 nstxout = 10000 nstenergy = 10000 ---
**Author:** ![Reza](https://avatars.discourse-cdn.com/v4/letter/r/b4bc9f/32.png) [@Reza](https://gromacs.bioexcel.eu/u/Reza)\ **Post date:** [April 5, 2022, 3:13pm UTC](https://gromacs.bioexcel.eu/t/why-is-it-different-every-time-the-interaction-energy-is-calculated/3956/2 "2022-04-05T15:13:13Z")
Why nobody answers me? The question is not complicated. ---
**Author:** ![Reza](https://avatars.discourse-cdn.com/v4/letter/r/b4bc9f/32.png) [@Reza](https://gromacs.bioexcel.eu/u/Reza)\ **Post date:** [April 5, 2022, 5:27pm UTC](https://gromacs.bioexcel.eu/t/why-is-it-different-every-time-the-interaction-energy-is-calculated/3956/3 "2022-04-05T17:27:40Z")
@jalemkul @alevilla @hess ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [April 5, 2022, 7:07pm UTC](https://gromacs.bioexcel.eu/t/why-is-it-different-every-time-the-interaction-energy-is-calculated/3956/4 "2022-04-05T19:07:53Z")
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. ---
**Author:** ![gvigers](https://avatars.discourse-cdn.com/v4/letter/g/a9a28c/32.png) [@gvigers](https://gromacs.bioexcel.eu/u/gvigers)\ **Post date:** [April 5, 2022, 7:09pm UTC](https://gromacs.bioexcel.eu/t/why-is-it-different-every-time-the-interaction-energy-is-calculated/3956/5 "2022-04-05T19:09:07Z")
Hi Reza 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? Best Wishes Guy Vigers ---
**Author:** ![Reza](https://avatars.discourse-cdn.com/v4/letter/r/b4bc9f/32.png) [@Reza](https://gromacs.bioexcel.eu/u/Reza)\ **Post date:** [April 5, 2022, 7:41pm UTC](https://gromacs.bioexcel.eu/t/why-is-it-different-every-time-the-interaction-energy-is-calculated/3956/6 "2022-04-05T19:41:15Z")
> [@hess](#): > > -reprod flag 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? ---
**Author:** ![Reza](https://avatars.discourse-cdn.com/v4/letter/r/b4bc9f/32.png) [@Reza](https://gromacs.bioexcel.eu/u/Reza)\ **Post date:** [April 5, 2022, 7:48pm UTC](https://gromacs.bioexcel.eu/t/why-is-it-different-every-time-the-interaction-energy-is-calculated/3956/7 "2022-04-05T19:48:33Z")
> [@gvigers](#): > > Guy Vigers Dear Guy Vigers, the command I use every time is below: **first simulation** gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt1.tpr gmx mdrun -v -deffnm nvt1 -nb cpu -pme cpu -pmefft cpu -bonded cpu -update cpu -pin auto -tunepme yes -reseed 123456789 -dlb yes gmx grompp -f Interaction\_energy.mdp -c nvt1.gro -p topol.top -o Interaction.tpr gmx mdrun -s Interaction.tpr -rerun nvt1.xtc -nt 1 gmx energy -f ener1.edr -o Interactionenergy1.xvg \> Interaction1.log **Second one** gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt2.tpr gmx mdrun -v -deffnm nvt2 -nb cpu -pme cpu -pmefft cpu -bonded cpu -update cpu -pin auto -tunepme yes -reseed 123456789 -dlb yes gmx grompp -f Interaction\_energy.mdp -c nvt2.gro -p topol.top -o Interaction.tpr gmx mdrun -s Interaction.tpr -rerun nvt2.xtc -nt 1 gmx energy -f ener2.edr -o Interactionenergy2.xvg \> Interaction2.log ---
**Author:** ![gvigers](https://avatars.discourse-cdn.com/v4/letter/g/a9a28c/32.png) [@gvigers](https://gromacs.bioexcel.eu/u/gvigers)\ **Post date:** [April 5, 2022, 8:11pm UTC](https://gromacs.bioexcel.eu/t/why-is-it-different-every-time-the-interaction-energy-is-calculated/3956/8 "2022-04-05T20:11:15Z")
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. Guy ---
**Author:** ![Reza](https://avatars.discourse-cdn.com/v4/letter/r/b4bc9f/32.png) [@Reza](https://gromacs.bioexcel.eu/u/Reza)\ **Post date:** [April 6, 2022, 8:08am UTC](https://gromacs.bioexcel.eu/t/why-is-it-different-every-time-the-interaction-energy-is-calculated/3956/9 "2022-04-06T08:08:20Z")
The interaction1 is not equal interaction2. The final coordinate about the same.