GROMACS version: 2023.1
GROMACS modification:No
Hi
im trying to run this line:
gmx_mpi grompp -f ions.mdp -c beta_solvated.gro -p topol.top -o beta_pp_ionize.tpr
And the following error comes up. I don’t understand why, of course there a charge, that’s why I want to add ions.
I’m using amber99sb-ildn FF.
Thanks!
Ignoring obsolete mdp entry ‘ns_type’
Setting the LD random seed to 1434415062
Generated 2145 of the 2145 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2145 of the 2145 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘Protein’
Excluding 2 bonded neighbours molecule type ‘SOL’
NOTE 1 [file topol.top, line 1089]:
System has non-zero total charge: -2.000000
Total charge should normally be an integer. See
Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation
for discussion on how close it should be to an integer.
WARNING 1 [file topol.top, line 1089]:
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: 9 Protein residues
There are: 2578 Water residues
Analysing Protein…
Number of degrees of freedom in T-Coupling group rest is 23523.00
The integrator does not provide a ensemble temperature, there is no system ensemble temperature
The largest distance between excluded atoms is 0.405 nm between atom 23 and 31
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 42x42x42, spacing 0.116 0.116 0.116
Estimate for the relative computational load of the PME mesh part: 0.25
This run will generate roughly 2 Mb of data
There was 1 NOTE
There was 1 WARNING
Program: gmx grompp, version 2023.1
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2691)
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 Common Errors — GROMACS webpage https://www.gromacs.org documentation
Abort(1) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0