GROMACS version: 2023
GROMACS modification: No
Hello everyone,
I am encountering a segmentation fault error while running gmx grompp. Here are the details of my setup and the error messages I am receiving:
Commands Executed
- Preparation of the
.tprfile:
gmx grompp -f nvt.mdp -c gromacs.gro -o gromacs_try.tpr -n index.ndx -p gromacs.top -maxwarn 5
Error Messages
During the execution of gmx mdrun, I receive the following error:
:-) GROMACS - gmx grompp, 2023 (-:
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Command line:
gmx grompp -f nvt.mdp -c gromacs.gro -o gromacs_try.tpr -n index.ndx -p gromacs.top -maxwarn 5
Setting the LD random seed to 1875893429
Generated 1275 of the 1275 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 1275 of the 1275 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘system1’
turning H bonds into constraints…
Excluding 3 bonded neighbours molecule type ‘72Y’
turning H bonds into constraints…
Excluding 3 bonded neighbours molecule type ‘Na+’
turning H bonds into constraints…
Excluding 3 bonded neighbours molecule type ‘Cl-’
turning H bonds into constraints…
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘Cl-’
Excluding 3 bonded neighbours molecule type ‘Na+’
Excluding 3 bonded neighbours molecule type ‘WAT’
turning H bonds into constraints…
NOTE 1 [file gromacs.top, line 36940]:
System has non-zero total charge: 0.004001
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 gromacs.top, line 36940]:
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 — -------- --------
Setting gen_seed to -457179185
Velocities were taken from a Maxwell distribution at 300 K
Cleaning up constraints and constant bonded interactions with virtual sites
Number of degrees of freedom in T-Coupling group Protein_72Y is 8278.72
Number of degrees of freedom in T-Coupling group Water_Na+_Cl- is 79014.28
The largest distance between excluded atoms is 0.427 nm between atom 22 and 30
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
Segmentation fault (core dumped)
Attached files
- nvt.mdp
nvt.mdp (6.5 KB) - gromacs.top
gromacs.top (1.8 MB)
If you need I can also share the file gromacs.gro and index.ndx
Request for Help
Has anyone encountered similar issues or have suggestions on how to resolve this problem? Any advice would be greatly appreciated!
Thank you in advance for your help!
Antonio