Dear all, I have worked with the same commands and setting in previous version of ubuntu and gromacs. Now with new system and up-gradation, I am facing problem. First kindly see the gmx information and then see the fatal error, I am getting at grompp. Kindly find the attached ions.mdp as well and see the other .mdp files too and guide me. Thanks & Regards Kalpana
1. gmx --version GROMACS version: 2019.3 Precision: single Memory model: 64 bit MPI library: thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support: CUDA SIMD instructions: AVX_512 FFT library: fftw-3.3.8-sse2-avx RDTSCP usage: enabled TNG support: enabled Hwloc support: hwloc-1.11.6 Tracing support: disabled C compiler: /usr/bin/gcc GNU 8.3.0 C compiler flags: -mavx512f -mfma -g -fno-inline C++ compiler: /usr/bin/c++ GNU 8.3.0 C++ compiler flags: -mavx512f -mfma -std=c++11 -g -fno-inline CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on Wed_Apr_24_19:10:27_PDT_2019;Cuda compilation tools, release 10.1, V10.1.168 CUDA compiler flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_75,code=compute_75;-use_fast_math;-D_FORCE_INLINES;; ;-mavx512f;-mfma;-std=c++11;-g;-fno-inline; CUDA driver: 10.10 CUDA runtime: N/A 2. gmx pdb2gmx -f 1model1A1.pdb -o model1_processed.gro -water tip3p no warning and notes in pdb2gmx run 3. gmx editconf -f model1_processed.gro -o model1_newbox.gro -c -d 1.0 -bt dodecahedron no warning and notes in editconf 4. gmx solvate -cp model1_newbox.gro -cs spc216.gro -o model1_solv.gro -p topol.top WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. NOTE: From version 5.0 gmx solvate uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- 5. gmx grompp -f ions.mdp -c model1_solv.gro -p topol.top -o ions.tpr NOTE 1 [file topol.top, line 60959]: System has non-zero total charge: -13.000000 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. WARNING 1 [file topol.top, line 60959]: You are using Ewald electrostatics in a system with net charge. This can lead to severe artifacts, such as ions moving into regions with low dielectric, due to the uniform background charge. We suggest to neutralize your system with counter ions, possibly in combination with a physiological salt concentration. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge J. Chem. Theory Comput. 10 (2014) pp. 381-393 -------- -------- --- Thank You --- -------- -------- Removing all charge groups because cutoff-scheme=Verlet Analysing residue names: There are: 424 Protein residues There are: 16060 Water residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 115683.00 Calculating fourier grid dimensions for X Y Z Using a fourier grid of 80x80x80, spacing 0.116 0.116 0.116 Estimate for the relative computational load of the PME mesh part: 0.34 This run will generate roughly 4 Mb of data There was 1 note There was 1 warning ------------------------------------------------------- Program: gmx grompp, version 2019.3 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2315) Fatal error: Too many warnings (1). If you are sure all warnings are harmless, use the -maxwarn option. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -------------------------------------------------------
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