GROMACS version: 2024.2
GROMACS modification: Yes/No
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Command line:
gmx_mpi mdrun -v -deffnm em
Back Off! I just backed up em.log to ./#em.log.2#
Reading file em.tpr, VERSION 2024.1 (single precision)
Update groups can not be used for this system because atoms that are (in)directly constrained together are interdispersed with other atoms
Using 1 MPI process
Using 32 OpenMP threads
Back Off! I just backed up em.trr to ./#em.trr.2#
Back Off! I just backed up em.edr to ./#em.edr.2#
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 5000
Step= 0, Dmax= 1.0e-02 nm, Epot= 2.33906e+18 Fmax= inf, atom= 252478
Step= 1, Dmax= 1.0e-02 nm, Epot= 2.33887e+18 Fmax= inf, atom= 252478
Step= 2, Dmax= 1.2e-02 nm, Epot= 2.33887e+18 Fmax= inf, atom= 252478
Step= 3, Dmax= 1.4e-02 nm, Epot= 2.33885e+18 Fmax= inf, atom= 252478
Step= 4, Dmax= 1.7e-02 nm, Epot= 2.33885e+18 Fmax= inf, atom= 252478
Step= 19, Dmax= 1.3e-06 nm, Epot= 2.33885e+18 Fmax= inf, atom= 252478
Energy minimization has stopped because the force on at least one atom is not
finite. This usually means atoms are overlapping. Modify the input
coordinates to remove atom overlap or use soft-core potentials with the free
energy code to avoid infinite forces.
You could also be lucky that switching to double precision is sufficient to
obtain finite forces.
writing lowest energy coordinates.
Back Off! I just backed up em.gro to ./#em.gro.2#
Steepest Descents converged to machine precision in 20 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 2.3388481e+18
Maximum force = inf on atom 252478
Norm of force = inf
The protein is a pentamer with 2 ligands and cations(present in each monomer).
The GROMACS input file was prepared using charmm gui.
The size of the monomer : 42kDa
How can i resolve this error?