normal Segmentation fault (core dumped)

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3 years 6 months ago #8791 by bayıl
Segmentation fault (core dumped) was created by bayıl
I created my dsdna pdb structure Nflex.Then I applied martini dna tutorial on my dsdna structure.
gmx grompp -f mdrun.mdp -c 02-eq.gro -p cg-dna.top -o 03-run

gmx mdrun -v -deffnm 03-run -rdd 2.0
after last these commands,it gives "Segmentation fault (core dumped)"
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ -nan, -nan, -nan}
Box[ 1]={ -nan, -nan, -nan}
Box[ 2]={ -nan, -nan, -nan}
Can not fix pbc.
how to fix ? Could you help me please ?

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3 years 6 months ago #8795 by vainikka
Replied by vainikka on topic Segmentation fault (core dumped)
Hi,

The errors GROMACS has given you indicate that your system has blown up. This can be the result of poor minimization and equilibration, or faulty topology. If you managed to run an equilibration simulation, then you can try running the simulation with a lower time step to see if you can figure out what makes the system unstable.

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2 years 8 months ago #9176 by saini
Replied by saini on topic Segmentation fault (core dumped)
Hi bayıl,
I am also getting the same error during NPT equilibration, if you you findout the solution of this error, please let me know.
If anyone knows how to fix this error please let me know, it would be great help for me.

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