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运行如下命令时：gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr
出现以下严重警告，最终导致报错：
WARNING 1 [file topol.top, line 11187]: 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.
报错内容：
Fatal error:
Too many warnings (1).
If you are sure all warnings are harmless, use the -maxwarn option.
请问我可以直接利用-maxwarn命令跳过这个警告吗？
结尾附上运行完整内容：
[root@192 CXCL8_5d]# gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr
:-) GROMACS - gmx grompp, 2020.6 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx grompp, version 2020.6
Executable: /opt/gromacs-2020.6/bin/gmx_mpi
Data prefix: /opt/gromacs-2020.6
Working dir: /home/moi/gromacs_MD/1/CXCL8_5d
Command line:
gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'ns_type'
NOTE 1 [file em.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
Setting the LD random seed to -549787922
Generated 3003 of the 3003 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 3003 of the 3003 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'ligand'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'CL'
NOTE 2 [file topol.top, line 11187]:
System has non-zero total charge: 0.001000
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 11187]:
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 --- -------- --------
Analysing residue names:
There are: 70 Protein residues
There are: 1 Other residues
There are: 6990 Water residues
There are: 4 Ion residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group rest is 45582.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 52x52x52, spacing 0.117 0.117 0.117
Estimate for the relative computational load of the PME mesh part: 0.18
This run will generate roughly 2 Mb of data
There were 2 notes
There was 1 warning
-------------------------------------------------------
Program: gmx grompp, version 2020.6
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2353)
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
-------------------------------------------------------
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
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发表于 Post on 2024-1-26 14:16:57
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发表于 Post on 2024-1-27 00:44:35
