[gmx-users] Fetal error at grompp

[Mark Abraham]

Hi,

Grompp is warning you that a periodic unit cell with a net charge of -13
doesn't model anything physical. Your earlier case was different, eg. you
added ions to neutralise the charge.

Mark

On Tue., 25 Jun. 2019, 09:05 kalpana, <kalpanadynasty at gmail.com> wrote:

> 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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