关于使用Gromacs模拟md却反复出现step 0Segmentation fault (core dumped)的问题

WangLeilei

本人在用Gromacs计算LiCl-NaF水溶液体系时用能量最小化之后的生成的gro文件生成tpr，出现两个Warning和Note
Command line:
  gmx grompp -f md.mdp -c NaLi_min.gro -p LiNa_min.top -o LiNa_md.tpr -maxwarn 3

WARNING 1 [file LiNa_min.top, line 14]:
  52544 non-matching atom names
  atom names from LiNa_min.top will be used
  atom names from NaLi_min.gro will be ignored


Removing all charge groups because cutoff-scheme=Verlet

NOTE 1 [file LiNa_min.top, line 14]:
  In moleculetype 'LiNa_min' 1675 atoms are not bound by a potential or
  constraint to any other atom in the same moleculetype. Although
  technically this might not cause issues in a simulation, this often means
  that the user forgot to add a bond/potential/constraint or put multiple
  molecules in the same moleculetype definition by mistake. Run with -v to
  get information for each atom.

Analysing residue names:
There are:     1      Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group System is 157629.00
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298.15 K
Calculated rlist for 1x1 atom pair-list as 1.005 nm, buffer size 0.005 nm
Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup

WARNING 2 [file md.mdp]:
  You are using full electrostatics treatment PME for a system without
  charges.
  This costs a lot of performance for just processing zeros, consider using
  Cut-off instead.


Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 72x72x72, spacing 0.113 0.113 0.113
Estimate for the relative computational load of the PME mesh part: 0.06

NOTE 2 [file md.mdp]:
  This run will generate roughly 2064 Mb of data

然后开始md模拟却反复出现step 0Segmentation fault (core dumped)的问题

Command line:
  gmx mdrun -v -nt 8 -s LiNa_md.tpr


Back Off! I just backed up md.log to ./#md.log.1#
Compiled SIMD: None, but for this host/run AVX2_128 might be better (see log).
The current CPU can measure timings more accurately than the code in
gmx mdrun was configured to use. This might affect your simulation
speed as accurate timings are needed for load-balancing.
Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
Reading file LiNa_md.tpr, VERSION 2018.4 (single precision)
Changing nstlist from 10 to 100, rlist from 1 to 1.106


Using 1 MPI thread
Using 8 OpenMP threads


WARNING: Oversubscribing the available 4 logical CPU cores with 8 threads.
         This will cause considerable performance loss.

NOTE: Oversubscribing the CPU, will not pin threads

WARNING: Using the slow plain C kernels. This should
not happen during routine usage on supported platforms.

Back Off! I just backed up ener.edr to ./#ener.edr.1#

WARNING: This run will generate roughly 2062 Mb of data

starting mdrun 'LiNa_min'
10000 steps,     10.0 ps.

Step 0  Warning: pressure scaling more than 1%, mu: 994.822 994.822 994.822
step 0Segmentation fault (core dumped)


尝试了很多次，用其他文件可以计算，只有这个体系不行，还望各位赐教

student0618

手机没法看附件，但见帖中top是LiNa， gro是NaLi 。两个文件的顺序是否一致？

JinxrDK

看起来像是体系没有完全平衡导致的
  :-) GROMACS - gmx mdrun, 2025.1 (-:

Executable:   /home/XXX/SOFTWARE/GROMACS2025/bin/gmx
Data prefix:  /home/XXX/SOFTWARE/GROMACS2025
Working dir:  /mnt/c/Users/XXX/Downloads/LiNa
Command line:
  gmx mdrun -deffnm topol -v


Back Off! I just backed up topol.log to ./#topol.log.4#
Reading file topol.tpr, VERSION 2025.1 (single precision)
Changing nstlist from 10 to 100, rlist from 1 to 1.068

Using 28 MPI threads
Using 1 OpenMP thread per tMPI thread


Back Off! I just backed up topol.xtc to ./#topol.xtc.4#

Back Off! I just backed up topol.trr to ./#topol.trr.4#

Back Off! I just backed up topol.edr to ./#topol.edr.4#

WARNING: This run will generate roughly 2062 Mb of data

starting mdrun 'xyz'
10000 steps,     10.0 ps.

Step 0  Warning: pressure scaling more than 1%, mu: 17486.8 17486.8 17486.8

Step 0  Warning: pressure scaling more than 1%, mu: 17486.8 17486.8 17486.8

Step 0  Warning: pressure scaling more than 1%, mu: 17486.8 17486.8 17486.8

Step 0  Warning: pressure scaling more than 1%, mu: 17486.8 17486.8 17486.8

Step 0  Warning: pressure scaling more than 1%, mu: 17486.8 17486.8 17486.8

Step 0  Warning: pressure scaling more than 1%, mu: 17486.8 17486.8 17486.8

Step 0  Warning: pressure scaling more than 1%, mu: 17486.8 17486.8 17486.8

Step 0  Warning: pressure scaling more than 1%, mu: 17486.8 17486.8 17486.8

Step 0  Warning: pressure scaling more than 1%, mu: 17486.8 17486.8 17486.8

Step 0  Warning: pressure scaling more than 1%, mu: 17486.8 17486.8 17486.8

Step 0  Warning: pressure scaling more than 1%, mu: 17486.8 17486.8 17486.8

Step 0  Warning: pressure scaling more than 1%, mu: 17486.8 17486.8 17486.8

Step 0  Warning: pressure scaling more than 1%, mu: 17486.8 17486.8 17486.8

Step 0  Warning: pressure scaling more than 1%, mu: 17486.8 17486.8 17486.8

Step 0  Warning: pressure scaling more than 1%, mu: 17486.8 17486.8 17486.8

Step 0  Warning: pressure scaling more than 1%, mu: 17486.8 17486.8 17486.8

Step 0  Warning: pressure scaling more than 1%, mu: 17486.8 17486.8 17486.8

Step 0  Warning: pressure scaling more than 1%, mu: 17486.8 17486.8 17486.8

Step 0  Warning: pressure scaling more than 1%, mu: 17486.8 17486.8 17486.8

-------------------------------------------------------
Program:     gmx mdrun, version 2025.1
Source file: src/gromacs/ewald/pme_redistribute.cpp (line 311)
MPI rank:    27 (out of 28)

Fatal error:
113 particles communicated to PME rank 3 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.

For more information and tips for troubleshooting, please check the GROMACS
website at https://manual.gromacs.org/curre ... un-time-errors.html
-------------------------------------------------------

Step 0  Warning: pressure scaling more than 1%, mu: 17486.8 17486.8 17486.8

Step 0  Warning: pressure scaling more than 1%, mu: 17486.8 17486.8 17486.8

Step 0  Warning: pressure scaling more than 1%, mu: 17486.8 17486.8 17486.8

Step 0  Warning: pressure scaling more than 1%, mu: 17486.8 17486.8 17486.8

Step 0  Warning: pressure scaling more than 1%, mu: 17486.8 17486.8 17486.8

WangLeilei

JinxrDK 发表于 2025-10-9 17:03
看起来像是体系没有完全平衡导致的
  :-) GROMACS - gmx mdrun, 2025.1 (-:

好的谢谢，那请问是需要重新能量最小化吗

JinxrDK

WangLeilei 发表于 2025-10-9 17:14
好的谢谢，那请问是需要重新能量最小化吗

我早上仔细看了下，大概是这么几个问题：
1）生成的水分子原子类型不一致，有几个(o, UF_H, os)原子类型莫名其妙，导致键能和其他水分子不一致，例如：
4468    4470         1        0.097300     3.107875E+05     ; O4468-H4470, prebuilt ho-oh
4471    4473         1        0.098100     2.994907E+05     ; O4471-H4473, prebuilt ho-o9（错误，替换为3.107875E+05）
2) [ atoms ]内的离子没有电荷，例如：
52200     UF_Li      1      MOL     Li52200   52200    0.00000000    6.940037
52200     UF_Li      1      MOL     Li52200   52200    1.00000000    6.940037（加上电荷）
3）[ bonds ]和[ dihedrals] 里出现了一些离子溶液中不该出现的二面角和键项，例如：（全部删除）
5972   51367    5971    5973         9         0.000       0.00000    1     ; H5972-Na51367-O5971-H5973 (UF_H-UF_Na-oh-ho) missing
5971   51367    5972         1        30.816      5.000000E+02     ; O5971-Na51367-H5972 (oh-UF_Na-UF_H) missing and simply guessed
29153   51516         1     ; H29153-O29152-H29154-Na51516
全部修改后可以正常模拟

JinxrDK

用工具生成的top文件一定要仔细检查，没有问题了再做模拟

WangLeilei

JinxrDK 发表于 2025-10-10 10:12
用工具生成的top文件一定要仔细检查，没有问题了再做模拟

好的，非常感谢你！