# Rerunning a simulation changes the energy components **URL:** \ **Category:** User discussions\ **Tags:** mdrun\ **Created:** [June 8, 2022, 1:14pm UTC](https://gromacs.bioexcel.eu/t/rerunning-a-simulation-changes-the-energy-components/4281 "2022-06-08T13:14:45Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![Jacqueries](https://avatars.discourse-cdn.com/v4/letter/j/977dab/32.png) [@Jacqueries](https://gromacs.bioexcel.eu/u/Jacqueries)\ **Post date:** [June 8, 2022, 1:14pm UTC](https://gromacs.bioexcel.eu/t/rerunning-a-simulation-changes-the-energy-components/4281/1 "2022-06-08T13:14:45Z")
GROMACS version:2022 single GROMACS modification: No I have simulations for a glycosilated protein dimer. There is two types of sugar and two glycosilation by monomer so the dimer has 4 sugars. I performed a first simulation with: gmx mdrun -s changeMDP.tpr -deffnm MDRUN For the first frame I get this in the .log file (the .edr is the same): Energies (kJ/mol) ``` Bond U-B Proper Dih. Improper Dih. CMAP Dih. 1.07905e+04 2.87134e+04 3.29585e+04 1.53244e+03 -1.42534e+03 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 8.73737e+03 1.30080e+05 1.16829e+06 -1.25230e+07 3.58665e+04 Potential Kinetic En. Total Energy Conserved En. Temperature ``` -1.11074e+07 1.97155e+06 -9.13586e+06 -9.13539e+06 3.02867e+02 Pressure (bar) Constr. rmsd 3.65355e+02 5.01554e-06 When I rerun the same simulation with the same .tpr with: gmx mdrun -s changeMDP.tpr -rerun MDRUN.xtc -deffnm RERUN For the first frame of the .log file I obtain: Energies (kJ/mol) ``` Bond U-B Proper Dih. Improper Dih. CMAP Dih. 2.59153e+04 4.00655e+04 3.37678e+04 2.62683e+03 -1.33921e+03 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 9.13910e+03 1.30032e+05 1.23807e+06 -1.25310e+07 4.21402e+04 Potential ``` -1.10106e+07 Why do I obtain different results using -rerun using the same .tpr file ? Thanks a lot ! EDIT: Here is the content of the .mdp used for the creation of the .tpr: integrator = md dt = 0.002 nsteps = 1000000000 ; 1000 ns nstlog = 10000 nstxout = 0 nstvout = 0 nstfout = 0 nstcalcenergy = 100 nstenergy = 10000 nstxout-compressed = 10000 compressed-x-precision = 100 ; cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 coulombtype = pme rcoulomb = 1.2 vdwtype = Cut-off vdw-modifier = Force-switch rvdw\_switch = 1.0 rvdw = 1.2 ; tcoupl = Nose-Hoover tc\_grps = Protein\_with\_sugar non\_protein\_non\_sugar tau\_t = 1.0 1.0 ref\_t = 300 300 ; pcoupl = Parrinello-Rahman pcoupltype = isotropic tau\_p = 5.0 compressibility = 4.5e-5 ref\_p = 1.0 ; constraints = h-bonds constraint\_algorithm = LINCS continuation = yes ; nstcomm = 100 comm\_mode = linear comm\_grps = Protein\_with\_sugar non\_protein\_non\_sugar ; refcoord\_scaling = com energygrps = Protein\_with\_sugar non\_protein\_non\_sugar ---
**Author:** ![adq](https://avatars.discourse-cdn.com/v4/letter/a/aca169/32.png) [@adq](https://gromacs.bioexcel.eu/u/adq)\ **Post date:** [August 3, 2022, 10:41am UTC](https://gromacs.bioexcel.eu/t/rerunning-a-simulation-changes-the-energy-components/4281/2 "2022-08-03T10:41:09Z")
Hi Jaquieries, I am having exactlty the same problem as you report. Evaluating the energy of a single frame using the same tpr file with rerun vs regular run result in slightly (15%) different potential energies. Could someone let us know if we should specify a special any setting in the input script, or is this expected behaviour? Many thanks to the community in advance ---
**Author:** ![Jacqueries](https://avatars.discourse-cdn.com/v4/letter/j/977dab/32.png) [@Jacqueries](https://gromacs.bioexcel.eu/u/Jacqueries)\ **Post date:** [August 3, 2022, 12:26pm UTC](https://gromacs.bioexcel.eu/t/rerunning-a-simulation-changes-the-energy-components/4281/3 "2022-08-03T12:26:01Z")
Hi adq, I didn’t find any solution for this… I also had a strange result in the decomposition, some of the 1-4 Electrostatic and hydrophobic contribution were taking into account pairs of atoms that were extremely far from each other and were not linked in 1-4. I verified the simulation and the topolgy and theses atoms are not linked in any way. Do you find this bug in your results ? ( do you have computed the decomposition for groups that cannot interact in 1-4 but you still obtain a value ?) ---
**Author:** ![adq](https://avatars.discourse-cdn.com/v4/letter/a/aca169/32.png) [@adq](https://gromacs.bioexcel.eu/u/adq)\ **Post date:** [August 3, 2022, 12:31pm UTC](https://gromacs.bioexcel.eu/t/rerunning-a-simulation-changes-the-energy-components/4281/4 "2022-08-03T12:31:40Z")
Hi, No, I don’t think I experience the second bit. Did you try the run and the rerun both without any constrains? I thought it would be related to this. May be some experts can comment? Thanks! ---
**Author:** ![pbauer](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/pbauer/32/13_2.png) [@pbauer](https://gromacs.bioexcel.eu/u/pbauer)\ **Post date:** [August 3, 2022, 8:15pm UTC](https://gromacs.bioexcel.eu/t/rerunning-a-simulation-changes-the-energy-components/4281/5 "2022-08-03T20:15:31Z")
Hello, this sounds indeed strange. Could you open a bug report at [Issues · GROMACS / GROMACS · GitLab](http://gitlab.com/gromacs/gromacs/-/issues) and upload a minimum tpr and trajectory that reproduces the issue? We have recently fixed some issues with energy contributions from excluded atom pairs, and if something is going wrong there we need to know. As an additional test, could you check this with the most recent 2022.2 patch? Thanks for your help! Cheers Paul ---
**Author:** ![spoblete](https://avatars.discourse-cdn.com/v4/letter/s/7c8e57/32.png) [@spoblete](https://gromacs.bioexcel.eu/u/spoblete)\ **Post date:** [April 29, 2024, 1:49pm UTC](https://gromacs.bioexcel.eu/t/rerunning-a-simulation-changes-the-energy-components/4281/6 "2024-04-29T13:49:52Z")
Greetings. I would like to know if this issue was already solved since I observed the same problem using Gromacs 2021. Best regards, Simón