# Zero interaction energy from mdrun -rerun in GMX 2020 vs non zero energies in GMX 2018 **URL:** \ **Category:** User discussions\ **Tags:** mdrun\ **Created:** [June 22, 2021, 1:54pm UTC](https://gromacs.bioexcel.eu/t/zero-interaction-energy-from-mdrun-rerun-in-gmx-2020-vs-non-zero-energies-in-gmx-2018/2396 "2021-06-22T13:54:16Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![fkeller](https://avatars.discourse-cdn.com/v4/letter/f/ba9def/32.png) [@fkeller](https://gromacs.bioexcel.eu/u/fkeller)\ **Post date:** [June 22, 2021, 1:54pm UTC](https://gromacs.bioexcel.eu/t/zero-interaction-energy-from-mdrun-rerun-in-gmx-2020-vs-non-zero-energies-in-gmx-2018/2396/1 "2021-06-22T13:54:16Z")
GROMACS version: 2020.6 / 2018.8 GROMACS modification: No Dear Gromacs Users, My task: I am (re-)calculating the interaction energy (LJ SR + Coul SR) of two residues in a trajectory using mdrun -rerun with energy groups GRPX and GRPY containing indices of resid X and resid Y in separate index groups. My problem: In GMX version 2020 these interactions are all 0.0, while using the same procedure with GMX version 2018 results in reasonable (non zero) interaction energies. Interestingly, the self interactions residueX-residueX are non zero but huge (\>80000 kJ/mol in 2020 vs 270 kJ/mol in 2018) in version 2020. Solution? I’d guess that it is somehow related to some changes in the way -rerun works in GMX 2020, though I could not find anything in the release notes. Thanks in advance for any information! Best Fabian ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [June 22, 2021, 2:05pm UTC](https://gromacs.bioexcel.eu/t/zero-interaction-energy-from-mdrun-rerun-in-gmx-2020-vs-non-zero-energies-in-gmx-2018/2396/2 "2021-06-22T14:05:47Z")
Sounds like your 2020 calculation was done on a GPU, which does not support energy groups. Make sure you’re running only on CPU for `mdrun -rerun`. ---
**Author:** ![fkeller](https://avatars.discourse-cdn.com/v4/letter/f/ba9def/32.png) [@fkeller](https://gromacs.bioexcel.eu/u/fkeller)\ **Post date:** [June 22, 2021, 2:25pm UTC](https://gromacs.bioexcel.eu/t/zero-interaction-energy-from-mdrun-rerun-in-gmx-2020-vs-non-zero-energies-in-gmx-2018/2396/3 "2021-06-22T14:25:10Z")
That’s a good point, as GMX actually notes that in the logs, but both versions are compiled without gpu support and use thread\_mpi. From the log file (shortened): > GROMACS: gmx mdrun, version 2020.6 > Executable: /home/f/f\_kell07/software/gromacs\_analysis-2020.6/bin/gmx > Data prefix: /home/f/f\_kell07/software/gromacs\_analysis-2020.6 > Working dir: /scratch/tmp/f\_kell07/analysis\_mclattice/dppc\_330/testruns > Process ID: 119139 > Command line: > gmx -nocopyright mdrun -ntomp 8 -ntmpi 8 -v -rerun /scratch/tmp/f\_kell07/mdfiles\_mclattice/md\_trj/dppc\_330\_whole.xtc -s mdrerun\_resid1\_leaflet.tpr > > GROMACS version: 2020.6 > Verified release checksum is 2f568d8884e039acbc6b68722432516e0628be00c847969b7c905c8b53ef826f > Precision: single > Memory model: 64 bit > MPI library: thread\_mpi > OpenMP support: enabled (GMX\_OPENMP\_MAX\_THREADS = 64) > GPU support: disabled > SIMD instructions: AVX\_512 > FFT library: fftw-3.3.8-sse2-avx-avx2-avx2\_128-avx512 > RDTSCP usage: enabled > TNG support: enabled > Hwloc support: hwloc-2.2.0 > Tracing support: disabled > C compiler: /Applic.HPC/Easybuild/skylake/2020a/software/GCCcore/9.3.0/bin/cc GNU 9.3.0 > C compiler flags: -mavx512f -mfma -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG > C++ compiler: /Applic.HPC/Easybuild/skylake/2020a/software/GCCcore/9.3.0/bin/c++ GNU 9.3.0 > C++ compiler flags: -mavx512f -mfma -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG > > Running on 1 node with total 36 cores, 72 logical cores > Hardware detected: > CPU info: > Vendor: Intel > Brand: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz > Family: 6 Model: 85 Stepping: 4 > Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop\_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic > Number of AVX-512 FMA units: 2 > … > Multiple energy groups is not implemented for GPUs, falling back to the CPU. For better performance, run on the GPU without energy groups and then do gmx mdrun -rerun option on the trajectory with an energy group .tpr file. > Input Parameters: > integrator = md > tinit = 0 > dt = 0.002 > nsteps = 0 > init-step = 0 > simulation-part = 1 > nstcalcenergy = 100 > nstenergy = 100 > cutoff-scheme = Verlet > nstlist = 20 > pbc = xyz > periodic-molecules = false > verlet-buffer-tolerance = 0.005 > rlist = 1.2 > coulombtype = PME > coulomb-modifier = Potential-shift > rcoulomb-switch = 0 > rcoulomb = 1.2 > epsilon-r = 1 > epsilon-rf = inf > vdw-type = Cut-off > vdw-modifier = Force-switch > rvdw-switch = 1 > rvdw = 1.2 > DispCorr = No > table-extension = 1 > tcoupl = Nose-Hoover > nsttcouple = 20 > nh-chain-length = 1 > print-nose-hoover-chain-variables = false > pcoupl = Parrinello-Rahman > pcoupltype = Semiisotropic > nstpcouple = 20 > tau-p = 5 And here is the output from gmx energy… …from GMX 2018 > @ title “GROMACS Energies” > @ xaxis label “Time (ps)” > @ yaxis label “(kJ/mol)” > @TYPE xy > @ view 0.15, 0.15, 0.75, 0.85 > @ legend on > @ legend box on > @ legend loctype view > @ legend 0.78, 0.8 > @ legend length 2 > @ s0 legend “Potential” > @ s1 legend “Coul-SR:resid\_341-resid\_341” > @ s2 legend “LJ-SR:resid\_341-resid\_341” > @ s3 legend “Coul-14:resid\_341-resid\_341” > @ s4 legend “LJ-14:resid\_341-resid\_341” > @ s5 legend “Coul-SR:resid\_341-leaflet” > @ s6 legend “LJ-SR:resid\_341-leaflet” > @ s7 legend “Coul-14:resid\_341-leaflet” > @ s8 legend “LJ-14:resid\_341-leaflet” > @ s9 legend “Coul-SR:resid\_341-interleaflet” > @ s10 legend “LJ-SR:resid\_341-interleaflet” > @ s11 legend “Coul-14:resid\_341-interleaflet” > 0.000000 -569471.812500 347.489532 -58.237930 -574.714905 18.380203 -174.961395 -257.103912 0.000000 0.000000 1.774202 -22.761156 0.000000 > 1000.000000 -572068.000000 228.242523 -47.072948 -449.503845 34.441422 -134.704391 -294.663940 0.000000 0.000000 1.343589 -15.537995 0.000000 > 2000.000000 -566054.812500 270.467377 -41.391750 -478.206879 27.504395 -120.776375 -233.636124 0.000000 0.000000 2.779344 -60.008224 0.000000 > 3000.000000 -568577.000000 259.353149 -47.965710 -460.656738 40.298637 -169.074280 -266.141602 0.000000 0.000000 4.071910 -74.605553 0.000000 > 4000.000000 -568047.437500 306.153503 -55.144253 -511.083923 34.962753 -97.457947 -227.578644 0.000000 0.000000 2.914246 -53.402748 0.000000 From version 2020: > @ title “GROMACS Energies” > @ xaxis label “Time (ps)” > @ yaxis label “(kJ/mol)” > @TYPE xy > @ view 0.15, 0.15, 0.75, 0.85 > @ legend on > @ legend box on > @ legend loctype view > @ legend 0.78, 0.8 > @ legend length 2 > @ s0 legend “Potential” > @ s1 legend “Coul-SR:resid\_341-resid\_341” > @ s2 legend “LJ-SR:resid\_341-resid\_341” > @ s3 legend “Coul-14:resid\_341-resid\_341” > @ s4 legend “LJ-14:resid\_341-resid\_341” > @ s5 legend “Coul-SR:resid\_341-leaflet” > @ s6 legend “LJ-SR:resid\_341-leaflet” > @ s7 legend “Coul-14:resid\_341-leaflet” > @ s8 legend “LJ-14:resid\_341-leaflet” > @ s9 legend “Coul-SR:resid\_341-interleaflet” > 0.000000 -569472.875000 0.000000 0.000000 -574.715027 18.380203 0.000000 0.000000 0.000000 0.000000 0.000000 > 1000.000000 -572068.375000 0.000000 0.000000 -449.503754 34.441410 0.000000 0.000000 0.000000 0.000000 0.000000 > 2000.000000 -566056.687500 0.000000 0.000000 -478.206848 27.504377 0.000000 0.000000 0.000000 0.000000 0.000000 > 3000.000000 -568577.687500 0.000000 0.000000 -460.656616 40.298637 0.000000 0.000000 0.000000 0.000000 0.000000 > 4000.000000 -568048.500000 0.000000 0.000000 -511.084076 34.962761 0.000000 0.000000 0.000000 0.000000 0.000000 > 5000.000000 -567961.000000 0.000000 0.000000 -534.145630 22.905722 0.000000 0.000000 0.000000 0.000000 0.000000 > 6000.000000 -568862.187500 0.000000 0.000000 -478.079651 22.513742 0.000000 0.000000 0.000000 0.000000 0.000000 > 7000.000000 -569597.937500 0.000000 0.000000 -466.317657 31.928671 0.000000 0.000000 0.000000 0.000000 0.000000 Note that exactly the same input was used for both reruns. For GMX 2020 I tried using tpr files generated with 2020 and, additionally, generated with 2018. I also tried manually disabling all GPU calculations (with mdrun flags like -bonded cpu -nb cpu …). Is this maybe a bug? ---
**Author:** ![gvigers](https://avatars.discourse-cdn.com/v4/letter/g/a9a28c/32.png) [@gvigers](https://gromacs.bioexcel.eu/u/gvigers)\ **Post date:** [April 1, 2022, 6:32pm UTC](https://gromacs.bioexcel.eu/t/zero-interaction-energy-from-mdrun-rerun-in-gmx-2020-vs-non-zero-energies-in-gmx-2018/2396/4 "2022-04-01T18:32:25Z")
Was there any resolution of this problem? I’m seeing the same thing when I try and calculate interaction energies for a subset of water molecules. gmx hbonds works fine on the subset, but gmx energy -rerun -nb cpu gives all zeros. The same problem occurs with gromacs 2021.2 and 2022. ---
**Author:** ![fkeller](https://avatars.discourse-cdn.com/v4/letter/f/ba9def/32.png) [@fkeller](https://gromacs.bioexcel.eu/u/fkeller)\ **Post date:** [April 4, 2022, 8:28am UTC](https://gromacs.bioexcel.eu/t/zero-interaction-energy-from-mdrun-rerun-in-gmx-2020-vs-non-zero-energies-in-gmx-2018/2396/5 "2022-04-04T08:28:48Z")
Hey, I haven’t received feedback on this issue on any platform… In the end, I went back calculating the energies using Gromacs version 2018. Best Fabian ---
**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, 6:57pm UTC](https://gromacs.bioexcel.eu/t/zero-interaction-energy-from-mdrun-rerun-in-gmx-2020-vs-non-zero-energies-in-gmx-2018/2396/6 "2022-04-05T18:57:37Z")
Hi Fabian Thank you for your reply. I have applied to join the developers mailing list to see if I can help with this problem. Gromacs is a spectacular set of programs, so I’d love to squash what appears to be a real bug :) I’ll let you know if I make any headway. Best Wishes Guy Vigers ---
**Author:** ![gvigers](https://avatars.discourse-cdn.com/v4/letter/g/a9a28c/32.png) [@gvigers](https://gromacs.bioexcel.eu/u/gvigers)\ **Post date:** [April 11, 2022, 2:57pm UTC](https://gromacs.bioexcel.eu/t/zero-interaction-energy-from-mdrun-rerun-in-gmx-2020-vs-non-zero-energies-in-gmx-2018/2396/7 "2022-04-11T14:57:17Z")
Hi Fabian The developers have found and fixed my problem. Many thanks to @berkhess and @erik.lindahl for the great work! The fix should be out in 2022.1 Hopefully it will work for your case too. Best Wishes Guy Vigers ---
**Author:** ![fkeller](https://avatars.discourse-cdn.com/v4/letter/f/ba9def/32.png) [@fkeller](https://gromacs.bioexcel.eu/u/fkeller)\ **Post date:** [April 11, 2022, 3:10pm UTC](https://gromacs.bioexcel.eu/t/zero-interaction-energy-from-mdrun-rerun-in-gmx-2020-vs-non-zero-energies-in-gmx-2018/2396/8 "2022-04-11T15:10:16Z")
Great! Thanks for your efforts to find a working solution and also thanks to the developers! :-)