Hello,
I want to perform REMD simulations on a protein dimer solvated in different concentrations of urea. For this, first to create only water system I have created box and solvated in water. When I was running energy minimization, the system got crashed and got below error. The two monomers are placed at a distance in the system.
GROMACS: gmx mdrun, version 2021.4-Ubuntu-2021.4-2
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/ubuntu/Meenakshi/REMD-simulations/bcn-water
Command line:
gmx mdrun -v -deffnm em
Compiled SIMD: SSE4.1, but for this host/run AVX_512 might be better (see
log).
Reading file em.tpr, VERSION 2021.4-Ubuntu-2021.4-2 (single precision)
Using 1 MPI thread
Using 16 OpenMP threads
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
WARNING: Listed nonbonded interaction between particles 3910 and 3918
at distance 2.751 which is larger than the table limit 2.000 nm.
This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.
IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.
Step= 0, Dmax= 1.0e-02 nm, Epot= 1.27151e+33 Fmax= inf, atom= 4719
Segmentation fault (core dumped)
What can this be due to? How can I resolve it?