GROMACS+CP2K做QMMM时报错QMMM系统电荷和经典体系不匹配

脊人

[color=var(--darkreader-text-444444, #bdb7af)]运行QMMM时报错

Command line:
  gmx_d grompp -f md-qmmm-nvt.mdp -p topol.top -c conf.gro -t egfp-mm-nvt.trr -n index.ndx -o egfp-qmmm-nvt.tpr

Setting the LD random seed to -553754706

Generated 9591 of the 9591 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5

Generated 9591 of the 9591 1-4 parameter combinations

Excluding 3 bonded neighbours molecule type 'Protein_chain_A'

Excluding 1 bonded neighbours molecule type 'SOL'

Excluding 1 bonded neighbours molecule type 'SOL'

Excluding 1 bonded neighbours molecule type 'NA'

NOTE 1 [file topol.top, line 33983]:
  The bond in molecule-type Protein_chain_A between atoms 111 OG1 and 112
  HG1 has an estimated oscillational period of 9.0e-03 ps, which is less
  than 10 times the time step of 1.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.

Number of degrees of freedom in T-Coupling group System is 200994.00

QMMM Interface with CP2K is active, topology was modified!
Number of QM atoms: 19
Number of MM atoms: 98679
Total charge of the classical system (before modifications): 0.00000
Classical charge removed from QM atoms: -1.25321
Total charge of QMMM system (after modifications): 0.25321
Bonds removed: 54
Angles removed: 34
Dihedrals removed: 55
F_CONNBONDS (type 5 bonds) added: 20
QM-MM broken bonds found: 2


WARNING 1 [file md-qmmm-nvt.mdp]:
  Total charge of your QMMM system differs from classical system! Consider
  manually spreading -0.25321 charge over MM atoms nearby to the QM region


The largest distance between excluded atoms is 0.420 nm between atom 3382 and 3390

Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K

Calculated rlist for 1x1 atom pair-list as 1.212 nm, buffer size 0.012 nm

Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm

Note that mdrun will redetermine rlist based on the actual pair-list setup

Reading Coordinates, Velocities and Box size from old trajectory

Will read whole trajectory
trr version: GMX_trn_file (double precision)
Last frame         10 time  100.000   

Using frame at t = 100 ps

Starting time for run is 0 ps
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 84x84x84, spacing 0.119 0.119 0.119

Estimate for the relative computational load of the PME mesh part: 0.18

This run will generate roughly 58 Mb of data

There was 1 NOTE

There was 1 WARNING

-------------------------------------------------------
Program:     gmx grompp, version 2024.5
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2751)

Fatal error:
Too many warnings (1).
If you are sure all warnings are harmless, use the -maxwarn option.

按照提示之后将电荷分配到QM'区域附近的MM原子之后报错：


Command line:
  gmx_d grompp -f md-qmmm-nvt.mdp -p topol_updated3.top -c conf.gro -t egfp-mm-nvt.trr -n index.ndx -o egfp-qmmm-nvt.tpr

Setting the LD random seed to -20531349

Generated 9591 of the 9591 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5

Generated 9591 of the 9591 1-4 parameter combinations

Excluding 3 bonded neighbours molecule type 'Protein_chain_A'

Excluding 1 bonded neighbours molecule type 'SOL'

Excluding 1 bonded neighbours molecule type 'SOL'

Excluding 1 bonded neighbours molecule type 'NA'

NOTE 1 [file topol_updated3.top, line 33983]:
  System has non-zero total charge: -0.193634
  Total charge should normally be an integer. See
  https://manual.gromacs.org/current/user-guide/floating-point.html
  for discussion on how close it should be to an integer.




WARNING 1 [file topol_updated3.top, line 33983]:
  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 --- -------- --------


NOTE 2 [file topol_updated3.top, line 33983]:
  The bond in molecule-type Protein_chain_A between atoms 111 OG1 and 112
  HG1 has an estimated oscillational period of 9.0e-03 ps, which is less
  than 10 times the time step of 1.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.

Number of degrees of freedom in T-Coupling group System is 200994.00

QMMM Interface with CP2K is active, topology was modified!
Number of QM atoms: 19
Number of MM atoms: 98679
Total charge of the classical system (before modifications): -0.19363
Classical charge removed from QM atoms: -1.25321
Total charge of QMMM system (after modifications): 0.05957
Bonds removed: 54
Angles removed: 34
Dihedrals removed: 55
F_CONNBONDS (type 5 bonds) added: 20
QM-MM broken bonds found: 2


WARNING 2 [file md-qmmm-nvt.mdp]:
  Total charge of your QMMM system differs from classical system! Consider
  manually spreading -0.25321 charge over MM atoms nearby to the QM region


The largest distance between excluded atoms is 0.420 nm between atom 3382 and 3390

Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K

Calculated rlist for 1x1 atom pair-list as 1.212 nm, buffer size 0.012 nm

Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm

Note that mdrun will redetermine rlist based on the actual pair-list setup

Reading Coordinates, Velocities and Box size from old trajectory

Will read whole trajectory
trr version: GMX_trn_file (double precision)
Last frame         10 time  100.000   

Using frame at t = 100 ps

Starting time for run is 0 ps
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 84x84x84, spacing 0.119 0.119 0.119

Estimate for the relative computational load of the PME mesh part: 0.18

This run will generate roughly 58 Mb of data

There were 2 NOTEs

There were 2 WARNINGs

-------------------------------------------------------
Program:     gmx grompp, version 2024.5
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2751)

Fatal error:
Too many warnings (2).
If you are sure all warnings are harmless, use the -maxwarn option.


请教大家如何解决