# Error during Gromacs energy minimization **URL:** \ **Category:** User discussions\ **Tags:** forcefield, grompp, mdrun, simulation-setup\ **Created:** [April 9, 2023, 6:06am UTC](https://gromacs.bioexcel.eu/t/error-during-gromacs-energy-minimization/6146 "2023-04-09T06:06:14Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![Gupta](https://avatars.discourse-cdn.com/v4/letter/g/ad7895/32.png) [@Gupta](https://gromacs.bioexcel.eu/u/Gupta)\ **Post date:** [April 9, 2023, 6:06am UTC](https://gromacs.bioexcel.eu/t/error-during-gromacs-energy-minimization/6146/1 "2023-04-09T06:06:15Z")
GROMACS version: 2022.1 GROMACS modification: Yes/No Here post your question Dear Gromacs Community, ## I am getting the following error during energy minimization of my system using Gromacs 2022.1 version. Thank you for your help. I used the following command : gmx\_mpi mdrun -v -deffnm em ERROR: fatal error gromacs/2022.1 does not support sc-r-power = 48. System: My system contains ~2000 Proteins, 2 RNA chains, 2000 ZN+2 ions, 90 million water tip3p and 5000 Chloride ions. I tried two different things and none of these have worked: 1. I assigned the value of sc-r-power = 6 in the minim.mdp file while preparing em.tpr. It gave me the same error as above. 2. I prepared and ran the simulation with gromacs/2019.6 mdrun\_mpi. this gave me a different error: Memory allocation failed: std::bad\_alloc Here is topology file: ; Executable: /opt/apps/intel19/impi19\_0/gromacs/2022.1/bin/gmx ; Data prefix: /opt/apps/intel19/impi19\_0/gromacs/2022.1 … … ; Include forcefield parameters #include “./charmm36-jul2022.ff/forcefield.itp” ; Include chain topologies #include “topol\_Protein\_chain\_X.itp” #include “topol\_Protein\_chain\_X2.itp” #include “topol\_Protein\_chain\_X3.itp” #include “topol\_Protein\_chain\_X4.itp” #include “topol\_Protein\_chain\_X5.itp” #include “topol\_Protein\_chain\_X6.itp” … … #include “topol\_RNA\_chain\_X2629.itp” #include “topol\_RNA\_chain\_X2630.itp” #include “topol\_Other\_chain\_X2631.itp” topol\_Other\_chain\_X2631.itp contains ZN+2 info ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 0 ZN2 rtp ZN2 q +2.0 1 ZN 0 ZN2 ZN 1 2 65.37 ; qtot 2 Here is the em.log file for gromacs/2022.1 ``` Anca Hamuraru Vincent Hindriksen Aleksei Iupinov ``` Dimitrios Karkoulis Peter Kasson Jiri Kraus Per Larsson Justin A. Lemkul Viveca Lindahl Erik Marklund Pieter Meulenhoff Vedran Miletic Teemu Murtola Sander Pronk Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf ``` Coordinated by the GROMACS project leaders: Paul Bauer, Berk Hess, and Erik Lindahl ``` GROMACS: gmx mdrun, version 2022.1 Executable: /opt/apps/intel19/impi19\_0/gromacs/2022.1/bin/gmx\_mpi Data prefix: /opt/apps/intel19/impi19\_0/gromacs/2022.1 Working dir: /work2/07732/tg870312/frontera/aa\_capsid/tvgg\_capsid/capsid-rnp Process ID: 238312 Command line: gmx\_mpi mdrun -v -deffnm em GROMACS version: 2022.1 Precision: mixed Memory model: 64 bit MPI library: MPI OpenMP support: enabled (GMX\_OPENMP\_MAX\_THREADS = 256) GPU support: disabled SIMD instructions: AVX\_512 CPU FFT library: Intel MKL GPU FFT library: none RDTSCP usage: enabled TNG support: enabled Hwloc support: disabled Tracing support: disabled C compiler: /opt/intel/compilers\_and\_libraries\_2020.4.304/linux/mpi/intel64/bin/mpicc Intel 19.1.0.20200306 C compiler flags: -xCORE-AVX512 -qopt-zmm-usage=high -O3 -DNDEBUG C++ compiler: /opt/intel/compilers\_and\_libraries\_2020.4.304/linux/mpi/intel64/bin/mpicxx Intel 19.1.0.20200306 C++ compiler flags: -xCORE-AVX512 -qopt-zmm-usage=high -qopenmp -O3 -DNDEBUG Intel MKL version: 2020.0.1 Running on 4 nodes with total 224 cores, 224 processing units Cores per node: 56 Logical processing units per node: -56 - 56 OS CPU Limit / recommended threads to start per node: 56 Hardware detected on host c205-034.frontera.tacc.utexas.edu (the node of MPI rank 0): CPU info: Vendor: Intel Brand: Intel(R) Xeon(R) Platinum 8280 CPU @ 2.70GHz Family: 6 Model: 85 Stepping: 7 Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl avx512secondFMA 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 Hardware topology: Basic Packages, cores, and logical processors: [indices refer to OS logical processors] Package 0: [0] [2] [4] [6] [8] [10] [12] [14] [16] [18] [20] [22] [24] [26] [28] [30] [32] [34] [36] [38] [40] [42] [44] [46] [48] [50] [52] [54] Package 1: [1] [3] [5] [7] [9] [11] [13] [15] [17] [19] [21] [23] [25] [27] [29] [31] [33] [35] [37] [39] [41] [43] [45] [47] [49] [51] [53] [55] CPU limit set by OS: -1 Recommended max number of threads: 56 ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E. Lindahl GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers SoftwareX 1 (2015) pp. 19-25 -------- -------- — Thank You — -------- -------- ---
**Author:** ![al42and](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/al42and/32/1393_2.png) [@al42and](https://gromacs.bioexcel.eu/u/al42and)\ **Post date:** [April 15, 2023, 2:05pm UTC](https://gromacs.bioexcel.eu/t/error-during-gromacs-energy-minimization/6146/2 "2023-04-15T14:05:53Z")
Hi! Can you try GROMACS 2023? We improved our handling of such large systems in the recent release.