[gmx-users] Kindly help

kalpana kalpanadynasty at gmail.com
Mon Jun 24 16:19:41 CEST 2019

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

  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
CUDA driver:        10.10
CUDA runtime:       N/A

gmx pdb2gmx -f 1model1A1.pdb -o model1_processed.gro -water tip3p
no warning and notes in pdb2gmx run

gmx editconf -f model1_processed.gro -o model1_newbox.gro -c -d 1.0 -bt
no warning and notes in editconf

gmx solvate -cp model1_newbox.gro -cs spc216.gro -o model1_solv.gro -p

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.

A. Bondi
van der Waals Volumes and Radii
J. Phys. Chem. 68 (1964) pp. 441-451
-------- -------- --- Thank You --- -------- --------

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
  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.

J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof
Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a
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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