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标题: 求助：生成em.tpr文件时出现严重警告，导致错误 [打印本页]

作者
Author: MOI_001 时间: 2024-1-26 14:16
标题: 求助：生成em.tpr文件时出现严重警告，导致错误
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.

作者
Author: Seyilaxa 时间: 2024-1-26 14:40
系统的总电荷未中和，可以参考这里的回答：
http://bbs.keinsci.com/thread-19226-1-1.html

作者
Author: MOI_001 时间: 2024-1-26 14:45

Seyilaxa 发表于 2024-1-26 14:40
系统的总电荷未中和，可以参考这里的回答：
http://bbs.keinsci.com/thread-19226-1-1.html

请问如果提示System has non-zero total charge: 0.001000
是不是说明系统总电荷量小呢？可不可以用maxwarn来忽略这个警告呢？

作者
Author: Seyilaxa 时间: 2024-1-26 15:58

MOI_001 发表于 2024-1-26 14:45
请问如果提示System has non-zero total charge: 0.001000
是不是说明系统总电荷量小呢？可不可以用maxw ...

可以检查一下具体是哪一部分的电荷出现问题，一般影响不大可以-maxwarn忽略掉，看看模拟结果是否有异常。实在担心的话在拓扑文件里把-0.001的电荷随便分配给一个原子就行。

作者
Author: MOI_001 时间: 2024-1-26 22:05

Seyilaxa 发表于 2024-1-26 15:58
可以检查一下具体是哪一部分的电荷出现问题，一般影响不大可以-maxwarn忽略掉，看看模拟结果是否有异常。 ...

好的感谢

作者
Author: sobereva 时间: 2024-1-27 00:44
参考北京科音分子动力学与GROMACS培训班（http://www.keinsci.com/workshop/KGMX_content.html）的ppt：
(, 下载次数 Times of downloads: 20)

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