normal Segmentation fault (core dumped): Update groups can not be used for this system

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11 months 3 weeks ago #9657 by denniqo
Hey guys i am pretty new to Martini simulations and i hope you can help me. I want to simulate an Ion channel embedded in a bilayer. The structure i use is a cryo-EM structure. So i first prepare the structure using pdb2pqr and add all missing parts of the structure. After that i energy minimize the atomic structure in vacuum using gromacs. I take that structure an use martinize2 from vermouth to make a cg representation of the protein (martinize2 -f protein.pdb -dssp mkdssp -ff martini3001 -x protein-cg.pdb -o protein-cg.top -elastic -ef 500 -eu 1.0 -el 0.5 -ea 0 -ep 0 -scfix -maxwarn 1). The i proceed with insane.py to create an bilayer and add solvents and ions to the structure (insane -f protein-cg.pdb -o system.gro -p topol.top -pbc square -box 18,18,18 -l POPC:3 -l POPG:7 -u POPC:3 -u POPG:7 -center -sol W -salt 0.15 -dm 5). After that i want to proceed with the energy minimazation using following .mdp file:

integrator = steep
nsteps = 5000
emtol = 1000
emstep = 0.001

And at this step i get following error:

gmx mdrun -deffnm em -v
:-) GROMACS - gmx mdrun, 2023.1 (-:

Executable: /usr/local/bin/gmx
Data prefix: /usr/local
Working dir: /home/qoraj/Documents/CG_simulations/my_pipeline/only_mthk/em
Command line:
gmx mdrun -deffnm em -v


Back Off! I just backed up em.log to ./#em.log.4#
Reading file em.tpr, VERSION 2023.1 (single precision)
Update groups can not be used for this system because an incompatible virtual site type is used

Using 1 MPI thread
Using 8 OpenMP threads

Segmentation fault (core dumped)

And i have no clue what exactly these virtual sites are. I know that they are in my protein.itp file at the end. Are there any solutions for this? Did i do something wrong in the preparation? I tried various things i also cant energy minimize the protein-cg structure in vacuum...

I hope somebody has had a similar error and knows the reasons for this error. I am happy for any advice.

Thanks!

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10 months 1 week ago #9668 by smith.12510
Hi,
This seems like a bug in the latest gromacs: gromacs.bioexcel.eu/t/segmentation-fault-core-dumped/6695/3
Best,
Harper

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