gmx ndx command can not output the new index file when i input a ndx file using Gromacs 2023
Summary
I use a software called gmx_MMPBSA to calculate the free energy. This software needs to separate the receptor group and ligand group by gmx ndx command. I get segmentation fault error when I run this command:
gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx
GROMACS version
GROMACS version: 2023
Precision: mixed
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 128)
GPU support: CUDA
NB cluster size: 8
SIMD instructions: AVX2_256
CPU FFT library: fftw-3.3.10-sse2-avx-avx2-avx2_128
GPU FFT library: cuFFT
Multi-GPU FFT: none
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
C compiler: /usr/bin/gcc-11 GNU 11.3.0
C compiler flags: -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -march=znver3 -Ofast -pipe -m64 -Wno-missing-field-initializers -O3 -DNDEBUG
C++ compiler: /usr/bin/g++-11 GNU 11.3.0
C++ compiler flags: -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -march=znver3 -Ofast -pipe -m64 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -O3 -DNDEBUG
BLAS library: External - detected on the system
LAPACK library: External - detected on the system
CUDA compiler: /opt/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2022 NVIDIA Corporation;Built on Wed_Sep_21_10:33:58_PDT_2022;Cuda compilation tools, release 11.8, V11.8.89;Build cuda_11.8.r11.8/compiler.31833905_0
CUDA compiler flags:-std=c++17;--generate-code=arch=compute_35,code=sm_35;--generate-code=arch=compute_37,code=sm_37;--generate-code=arch=compute_50,code=sm_50;--generate-code=arch=compute_52,code=sm_52;--generate-code=arch=compute_60,code=sm_60;--generate-code=arch=compute_61,code=sm_61;--generate-code=arch=compute_70,code=sm_70;--generate-code=arch=compute_75,code=sm_75;--generate-code=arch=compute_80,code=sm_80;--generate-code=arch=compute_86,code=sm_86;--generate-code=arch=compute_89,code=sm_89;--generate-code=arch=compute_90,code=sm_90;-Wno-deprecated-gpu-targets;--generate-code=arch=compute_53,code=sm_53;--generate-code=arch=compute_80,code=sm_80;-use_fast_math;-Xptxas;-warn-double-usage;-Xptxas;-Werror;-D_FORCE_INLINES;-fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -march=znver3 -Ofast -pipe -m64 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -O3 -DNDEBUG
CUDA driver: 12.0
CUDA runtime: 11.80Steps to reproduce
echo q|gmx make_ndx -f Production.gro -o index.ndx
Success, I get an index.ndxAnd Then:
:-) GROMACS - gmx make_ndx, 2023 (-:
Executable: /home/yangzichen/Software/GMX-2023/bin/gmx
Data prefix: /home/yangzichen/Software/GMX-2023
Working dir: /home/yangzichen/Documents/76G1_7.2
Command line:
gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx
Going to read 1 old index file(s)
Counted atom numbers up to 80055 in index file
0 System : 80055 atoms
1 Protein : 7165 atoms
2 Protein-H : 3598 atoms
3 C-alpha : 449 atoms
4 Backbone : 1347 atoms
5 MainChain : 1797 atoms
6 MainChain+Cb : 2219 atoms
7 MainChain+H : 2224 atoms
8 SideChain : 4941 atoms
9 SideChain-H : 1801 atoms
10 Prot-Masses : 7165 atoms
11 non-Protein : 72890 atoms
12 Other : 218 atoms
13 RD : 160 atoms
14 UPG : 58 atoms
15 NA : 92 atoms
16 CL : 79 atoms
17 Water : 72501 atoms
18 SOL : 72501 atoms
19 non-Water : 7554 atoms
20 Ion : 171 atoms
21 RD : 160 atoms
22 UPG : 58 atoms
23 NA : 92 atoms
24 CL : 79 atoms
25 Water_and_ions : 72672 atoms
nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups
'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues
't': atom type '|': or 'keep' nr 'splitat' nr 'h': help
'r': residue 'res' nr 'chain' char
"name": group 'case': case sensitive 'q': save and quit
'ri': residue index
> name
> 1
[1] 5809 segmentation fault (core dumped) gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx
Even I using:
:-) GROMACS - gmx make_ndx, 2023 (-:
Executable: /home/yangzichen/Software/GMX-2023/bin/gmx
Data prefix: /home/yangzichen/Software/GMX-2023
Working dir: /home/yangzichen/Documents/76G1_7.2
Command line:
gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx
Going to read 1 old index file(s)
Counted atom numbers up to 80055 in index file
0 System : 80055 atoms
1 Protein : 7165 atoms
2 Protein-H : 3598 atoms
3 C-alpha : 449 atoms
4 Backbone : 1347 atoms
5 MainChain : 1797 atoms
6 MainChain+Cb : 2219 atoms
7 MainChain+H : 2224 atoms
8 SideChain : 4941 atoms
9 SideChain-H : 1801 atoms
10 Prot-Masses : 7165 atoms
11 non-Protein : 72890 atoms
12 Other : 218 atoms
13 RD : 160 atoms
14 UPG : 58 atoms
15 NA : 92 atoms
16 CL : 79 atoms
17 Water : 72501 atoms
18 SOL : 72501 atoms
19 non-Water : 7554 atoms
20 Ion : 171 atoms
21 Water_and_ions : 72672 atoms
nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups
'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues
't': atom type '|': or 'keep' nr 'splitat' nr 'h': help
'r': residue 'res' nr 'chain' char
"name": group 'case': case sensitive 'q': save and quit
'ri': residue index
> 1|13
[1] 6313 segmentation fault (core dumped) gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx
What is the current bug behavior?
segmentation fault (core dumped)
What did you expect the correct behavior to be?
Successful output _GMXMMPBSA_COM_index.ndx, like GMX2021.7 GMX2021.6
Possible fixes I tested several versions before 2023, such as 2021.7
Edited by Zichen Yang