An error was encountered in the "Energy minimization" step

[zousiyu1995]

When I run commands in the "Energy minimization" step, there are some warnings and errors.

https://gromacstutorials.github.io/sphinx/build/html/tutorials/tutorial1/bulk-solution.html

C:\Users\zousiyu\Desktop\gromacs_tutorials\tutorial1> gmx grompp -f inputs/min.mdp -c conf.gro -o min -pp min -po
 min
                      :-) GROMACS - gmx grompp, 2025.1 (-:

Executable:   D:\bin\gromacs\bin\gmx.exe
Data prefix:  D:\bin\gromacs
Working dir:  C:\Users\zousiyu\Desktop\gromacs_tutorials\tutorial1
Command line:
  gmx grompp -f inputs/min.mdp -c conf.gro -o min -pp min -po min

Setting the LD random seed to 2130422999

Back Off! I just backed up min.top to ./#min.top.4#

Generated 21 of the 21 non-bonded parameter combinations

Excluding 1 bonded neighbours molecule type 'SO4'

Excluding 1 bonded neighbours molecule type 'Na'

Excluding 2 bonded neighbours molecule type 'SOL'

atom name 31 in topol.top and conf.gro does not match (Na1 - Na)
atom name 31 in topol.top and conf.gro does not match (Na1 - Na)

atom name 32 in topol.top and conf.gro does not match (Na1 - Na)

atom name 32 in topol.top and conf.gro does not match (Na1 - Na)

atom name 33 in topol.top and conf.gro does not match (Na1 - Na)

atom name 33 in topol.top and conf.gro does not match (Na1 - Na)

atom name 34 in topol.top and conf.gro does not match (Na1 - Na)

atom name 34 in topol.top and conf.gro does not match (Na1 - Na)

atom name 35 in topol.top and conf.gro does not match (Na1 - Na)

atom name 35 in topol.top and conf.gro does not match (Na1 - Na)

atom name 36 in topol.top and conf.gro does not match (Na1 - Na)

atom name 36 in topol.top and conf.gro does not match (Na1 - Na)

atom name 37 in topol.top and conf.gro does not match (Na1 - Na)

atom name 37 in topol.top and conf.gro does not match (Na1 - Na)

atom name 38 in topol.top and conf.gro does not match (Na1 - Na)

atom name 38 in topol.top and conf.gro does not match (Na1 - Na)

atom name 39 in topol.top and conf.gro does not match (Na1 - Na)

atom name 39 in topol.top and conf.gro does not match (Na1 - Na)

atom name 40 in topol.top and conf.gro does not match (Na1 - Na)

atom name 40 in topol.top and conf.gro does not match (Na1 - Na)

atom name 41 in topol.top and conf.gro does not match (Na1 - Na)

atom name 41 in topol.top and conf.gro does not match (Na1 - Na)

atom name 42 in topol.top and conf.gro does not match (Na1 - Na)

atom name 42 in topol.top and conf.gro does not match (Na1 - Na)

WARNING 1 [file topol.top, line 12]:
  12 non-matching atom names
  atom names from topol.top will be used
  atom names from conf.gro will be ignored



Cleaning up constraints and constant bonded interactions with virtual sites
Analysing residue names:
There are:    18      Other residues
There are:   800      Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group rest is 4923.00
The integrator does not provide a ensemble temperature, there is no system ensemble temperature

NOTE 1 [file inputs/min.mdp]:
  You are using a plain Coulomb cut-off, which might produce artifacts.
  You might want to consider using PME electrostatics.



This run will generate roughly 19 Mb of data

There was 1 NOTE

There was 1 WARNING

-------------------------------------------------------
Program:     gmx grompp, version 2025.1
Source file: src\gromacs\gmxpreprocess\grompp.cpp (line 2898)

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 https://manual.gromacs.org/current/user-guide/run-time-errors.html
-------------------------------------------------------

Next,

C:\Users\zousiyu\Desktop\gromacs_tutorials\tutorial1> gmx mdrun -v -deffnm min
                      :-) GROMACS - gmx mdrun, 2025.1 (-:

Executable:   D:\bin\gromacs\bin\gmx.exe
Data prefix:  D:\bin\gromacs
Working dir:  C:\Users\zousiyu\Desktop\gromacs_tutorials\tutorial1
Command line:
  gmx mdrun -v -deffnm min


-------------------------------------------------------
Program:     gmx mdrun, version 2025.1
Source file: src\gromacs\options\options.cpp (line 184)
Function:    void __cdecl gmx::internal::OptionSectionImpl::finish(void)

Error in user input:
Invalid input values
  In option s
    Required option was not provided, and the default file 'topol' does not
    exist or is not accessible.
    The following extensions were tried to complete the file name:
      .tpr

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

[lgx1718]

I have the same problem,how could you solve it?