[gmx-users] Kindly help

Tue Jun 25 14:09:53 CEST 2019

Dear Kalpana,

As you would note in the output files, grompp throws one warning . The way
warnings work in grompp is to not allow obviously inconsistent choices of
options. So if there is warning(s) while running grompp, no .tpr file is
generated. However, there may be some situations (as in your case too),
where you know that the warning is not relevant in the given context. For
such cases, grompp has a -maxwarn flag, which can be used to suppress these
warning and direct grompp to produce the .tpr file. In your case adding
-maxwarn 1 to grompp command should work.

Just a note of caution: -maxwarn flag should only be used when you are
quite sure that the warnings are really irrelevant, otherwise you risk
gross misuse of the flag. ;)

Hope this helps.
Abhishek

On Mon, Jun 24, 2019 at 4:19 PM 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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