Error during Gromacs energy minimization

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GROMACS version: 2022.1
GROMACS modification: Yes/No
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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 — -------- --------

2

Hi!

Can you try GROMACS 2023? We improved our handling of such large systems in the recent release.

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